We've flown with every one of the current non-stop options at some point - Airtran from Flint and Airtran, Spirit, and Delta from Detroit. They all have their downsides - Delta's price and having to deal with the big terminal, Spirit's fees for everything, Airtran's habit of changing flight schedules. I just go with whichever is cheapest, including all the nickle & diming, and pack my patience.
All things equal I'd much rather go out of Flint but Airtran's current schedule doesn't work for us and they've been consistantly quite a bit more expensive than going out of Detroit (like double or triple the DTW sale fares). I am really looking forward to seeing what happens with the routes and schedules once the Airtran-Southwest merger is complete, because if they offered a non-stop I'd take SW over all the current options.