I know quite a few folks who commute from Chapel Hill to Raleigh and it's really not that bad. DH used to do it, but has since gotten a job in CH so now he walks to work or takes the free bus. I think you should seriously figure out what you want as far as schools. Personally, I'd be pretty concerned about going into the Wake County schools right now. I'd rather do Durham if I had to choose between the two. That new Wake Co school board just does not give me a warm fuzzy feeling.
CH schools have an excellent reputation for public schools and the private schools in the area (including West Durham and Northern Chatham) are excellent with many progressive and alternative options (Waldorf and Friends among them). It's pretty common for folks around here to move to CH/C for the schools from other parts of the triangle. I also don't like a town as big and sprawly as Raleigh, but if you like the big city thing it might be a better fit for you. I like small towns so CH is better for me. I could go smaller, too, Pittsboro, Hillsborough, Carrboro (of course), Saxapahaw! There's also a great homeschooling community in Chapel Hill and Durham. I don't know as much about Raleigh because I'm not on the loop on that, but I have many homeschooling friends in CH and Durham, and when I say CH I mean Chapel Hill AND Carrboro, of course.
Raleigh has some very interesting stuff going on these days, especially downtown. I have a friend who lives in Five Points and she really likes it, but they don't have kids. I do think it's becoming more progressive culturally. I keep seeing events and thinking, wow that looks cool, but I really don't like the traffic in Raleigh to get to the events, so I usually stay in CH and Durham. Durham is much more driveable IMO. If I were going to choose a different town in the Triangle beside CH/C it would hands-down be Durham and I know my DH feels the same way. It's got a great progressive feel and I think they have some good stuff going on with the schools. I have a couple of friends who are pretty happy with the public/charter schools their kids are in.
Chapel Hill has a reputation of being much more expensive than Durham or Raleigh, even, but you can definitely find deals. I have a friend right now who is moving out of a rental in a sweet little neighborhood in Carrboro that goes for $1200 a month. It's walkable to the farmer's market, schools, local coop grocery store. It's 3-4 bedroom with a fenced in backyard, hardwood floors. It's older, but it's in a great little neighborhood with lots of kids. You can definitely buy a pretty good place for $250. You can drop $4 million, too, if you want to. I know of one that's for sale, but if that's out of your price range you can definitely buy a single family home in a nice neighborhood for $250 or maybe less. You can certainly spend more, but don't listen to folks who say you can't buy for less than $500 in Chapel Hill. You certainly can spend that much if you want to and get a very nice house, but you don't have to.
It's very LGBT friendly, with a huge local food movement in CH/Carrboro and Durham. Raleigh is starting to get on the local and organic food bandwagon, too, but CH/C have been leading the way for more than 30 years (Carrboro farmer's mkt was established in the 70s with organic growers from the get go). I've lost track of how many CSAs we have in the CH/C area. Durham has a sweet farmer's mkt now, too, started in '98. Raleigh has a big state sponsored farmer's mkt, too, which has seen an increase in organics in the past couple of years, but it started as just a very conventional big, big market, so it's got quite a different feel.
Overall, I think the three main Triangle cities are all great, but I definitely recommend renting and being open to all three. Folks commute from one to the other all the time and it's not that bad, but Raleigh, since it's a bigger city definitely has worse traffic. There are a lot of jobs in RTP, too. I think you can find your food needs anywhere in the triangle, but Orange county and Durham and Chatham are definitely the hubs. All three areas are pretty welcoming and have strong LGBT communities. Come on down, and take a look around, but take a close look at schools!