Yes; you can live anywhere you want, so there's no reason to be unpleasantly crowded- but there's also no reason to live in a tiny isolated community that is only accessible in a timely manner using supersonic flying cars
On a homeworld, small towns would tend to do a lot of 'drying up' in the local equivalent of the 20th and 21st centuries on Earth, unless deliberately preserved- we know this because it's already happening in real life. By the time transportation advantages make living 100 km from work as practical as living 10 km from work, those little towns have very little going for them relative to a suburb 10-20 km from an urban center.
A lot would depend on the exact balance of work, leisure, and the availability of resources within a given society. But on the whole, while I'm not saying that the logical outcome on a Star Trek planet is for everyone to live in ultra-dense hive-cities or anything... I strongly suspect that people would tend to clump up at least as much as in real life, if not more so. It's simply that they'd tend to clump into large, sprawling, low-density "metropolitan areas," not into gigantic arcologies.