Shujin, you know how I've stated when we were writing that the best lies are those that utilize the "Truth"?
Look at things from that perspective. Chaos manipulated Horus via a self-fulfilled prophecy that used a "Truth" without context. The IoM's xenophobia? Based on the fact that 98%-99.5% of the other races have fucked them over in various ways.
One or two examples of races that haven't fucked humanity over just because they could does not mean that the other ninety-eight are comparable to those two. Given that, it becomes easy to see how those contexts could shape things.
And as Pax_Empyrean pointed out, all the races in 40K are terrible. The Tau tend to sterilize the populations they conquer. The IoM is (somewhat justifiably) paranoid, schizophrenic, imperialistic, genocidal, disfunctional, and composed of a lot of different groups that would be fighting eachother if they didn't have everything else to worry about and fight against. The Eldar have fucked everyone over, and their messes are finally catching up with them. The Tyranids want as much biomass as possible to put between themselves and whatever they're (apparently?) running from. Chaos is Chaos. The Necrons/Newcrons are various bags of assholishness, omnicidal, isolationist, imperialistic, and trollish. The Orks just want to have a good scrap.
Out of all those groups, the group(s?) that is the 'least' evil are either the Orks who just want to fight, or the Tyranids, and that's just because all they want to do is eat you (and even then they too will use a lot of subterfuge and manipulation and mindfuckery and body-horror to accomplish that goal). :shrugs:
All of 40K's groups are terrible. And while not everything they say is truth, not everything they say is a lie either.