For Humans, Gensokyo is ... a fairly nice place. Life is pretty decent, for a pre-industrial society - though they do have magic to make things a lot easier, and some of the nicer youkai, like Eirin or Keine, do things that humans can't do or don't have the time for. The main strictures on humans are, of course, the youkai. Youkai - especially the very powerful and the very weak, are territorial; the weak because those territories are their hunting grounds, the powerful because those territories are their homes.
So there are definite - and defined - restrictions on where humans are allowed and not allowed to go; the Hakurei Mikos can attempt to negotiate with youkai if there's a problem, or someone can be hired to attempt to drive away or eliminate troublesome youkai. Marisa, for example - in her PMiSS article, it's mentioned that she makes a living exterminating youkai. Now, Marisa's pretty damn good at danmaku ... but an actual fight is going to be something else. She's a squishy human, even if she does have powerful magic from her Hakkero, and youkai above a certain level simply aren't going to have issues squashing her like a bug if she tries to exterminate them. Reimu can also perform these tasks, and she's better at it for a couple reasons: One, she's the Hakurei Miko, and therefore youkai are hesitant to actually fight her; two, even if they do fight her, she can avoid their attacks; three, youkai are inherently weak to faith-based attacks, and that's what most of Reimu's attacks are, so she can hit way above her weight class, since she doesn't need to worry about blasting through the sheer durability of powerful youkai the way Marisa would.
Of course, not all youkai are inherently hostile, and it depends on what you're doing .... For example, say you have a very sick child, and you need a certain herb to cure him. Unfortunately, said plant is only known to grow in Yuuka's garden. Well. You're just a poor squishy human, not some hero, so what're you gonna do? You've got a few options:
1) You can say "Forget it," and try to make the kid's last days comfortable.
2) You can try to hire or beg/persuade a professional to get if for you.
3) You can go yourself and try to get the plant.
Let's say you go with 3, because you're too poor to hire Marisa and Reimu is off solving some incident. How do you go about it? Well, you've got two basic options: Sneak or Be Obvious. If you sneak into Yuuka's territory, and she catches you doing it, Yuuka will happen to you. Bad End. So you shouldn't do that. Instead, what you should do is walk up the clearly marked path to her door and knock; she has a house (most 'civilized' youkai do), even if she doesn't need it, and she probably knew you where here the moment you entered her territory. She'll come ... probably. Eventually.
So let's say Yuuka's right there and not busy, so she lets you in and listens to your request for the plant. She has two options - Yes or No; "No" may lead to a second possibility, depending on how she phrases it. If she says "Yes" - unlikely, but possible - then she'll go get the herb for you and just hand it over; you'd better be grateful as hell, but she won't ask for anything in return (though she will take things if you offer them). If she says "No," there are two ways she can say it - "No, and get out," which means you should leave or Yuuka will happen to you, and "... Well, I would, but the plant is so very rare and precious to me ...." Which is code for "I'll let you have one, but you need to be able to pay me." Most youkai who enter the bargaining stage won't actually ask you for something you're not capable of doing, but they will make sure the bargain is fair ... from their side. For example, Yuuka might want another flower that she *could* get herself, but is too lazy/busy to get ... and said flower is in Eientei, which means you're going to have to talk to the Lunarians to get it, and probably bargain with them; or she may just want you to plant certain plants in certain locations and make sure they grow.
On the other hand, if you go to a human-friendly place like the Scarlet Devil Mansion, you generally have to really tick people off before they're willing to get hostile, and even then you're likely to be thrown out still alive. So let's say you need some information on something, so you go there because you've heard the Library there has information on just about everything. You go up to the Gate and talk to Meiling - possibly because you haven't quite realized she's actually a youkai herself - and she'll probably let you in, with a pass to go to the Library so the maids don't throw you out. Maybe you'll run across Remilia, because she likes talking to new people, but if you go during the day it's quite likely you won't meet anyone. So you make it down to the Library and meet Patchouli. Now, Pache doesn't like humans, but Remi's standing policy is that unless they do something against the rules, she can't do anything, so she'll listen to what you have to say. And, because Pache isn't going to give you something for free - you're a greedy human, after all - you're probably going to go straight to the bargaining stage. And that is going to be hard, because what can you offer Patchouli that she doesn't already know?
Most 'civil' youkai are going to be closer to Yuuka than Patchouli; they usually won't kill you out of hand, but you're certainly taking your life into your hands just going there, which is why people like Marisa can make a living doing intermediary work. Likewise, hedge-wizards and -witches who can't danmaku well but are still competent spell-casters can deal with lower youkai if they're prepared.
And full circle: Magic. Marisa's a pretty good magician, and she's got a lot of firepower with that Hakkero - if she gets the drop on a high-level Youkai and goes for the kill, she can do a lot of damage. She'll probably still die, because high-level youkai are just that tough, but she'll hurt it. In a straight-up fight, even mid-level youkai - Mystia, Letty, and the like - are going to be quite dangerous. A magician like Patchouli, on the other hand, is dangerous because she's powerful, but mainly because she could give D&D mages lessons in paranoid planning. If you get the drop on her, and she has no contingent defenses or you can bypass them somehow, you can beat her pretty easily. If she's not feeling well, Marisa can just Blazing Star through her barriers and smack her in the face with a broom for a OHKO ... but if she's feeling well and is prepared, she can go toe-to-toe with Remilia until one of them gets tired. Patchouli is not a lightweight as far as power levels in Gensokyo go, and if she's healthy and out for blood, she has the power, knowledge, and connections to put a lot of hurt where she wants to.
Humans can survive in Gensokyo, quite easily and comfortably ... so long as they understand and obey the rules that hold the place together. Step outside the "Safe for Human" zone? Better be prepared to fight, because you're fair game. Trash-talk a youkai because you're under the assumption that since humans are "protected" you're safe, even in the Safe Zones? Bad End For You. It's not a crapsack world, but it doesn't particularly tolerate stupidity.
But Youkai - most of them - need to do things; they need the fear, they get bored, and so on. Incidents using the Spell Card System help with this, and with inter-youkai political disputes (when they choose not to go for the kill, which still happens sometimes). Not all Incidents have a major effect on human lives - The Scarlet Mist and the Long Winter, for example, did, but the Imperishable Night and Mountain of Faith went completely unnoticed by humans (except those involved).