THere is no disadvantage whatsoever in acquiring fellowships with community programs. All of our chiefs got the fellowships of their choice last year and our fourth year class has, as well. Beneftis of community places, as bonedoc pointed out are that we operate a ton and do a lot less scut. I also like seeing real medicine, rather than academic medicine. We get to see how 40+ different attendings practice. We get to see what types of practices we like and what types we don't, we also get to see multiple ways to do something, rather than one or two that you typically see in an academic place with one or two guys per specialty.
You can choose community programs, or university affiliated when searching frieda to find the comuunity places. Although, some community programs are listed under academic for some reason. I interviewed at mostly community places, some of the best being Grand Rapids, Kalamazoo, Akron, Fort Wayne, Wichitaw, Mt. Caramel, Greenville, Carolinas, Beuamont, JPS, and Geisenger.