FRA is infact the main faction, but the Enclave chosen for this mission are highly trained for wasteland survival, and the absolute best combat trained and best armed outside of the Oil Rig (and Navarro). They're small due to this, giving balance to these advantages. It would simply be skill versus numbers. The fact is, though, FRA doesn't need to worry about the Enclave yet. Nor do nearly all. It will be a long time before the Enclave actually pose any danger to anyone who doesn't bother them. As for the Brotherhood, they are also very well trained, and almost as well armed. They have more numbers than the Enclave (or should). The FRA have numbers and support of the wastelanders, giving them a balance to the two factions who are better armed and trained. The FRA currently has the least numbers, though, which MUST be fixed. As stated, they should have by far the most numbers due to being the natives and the most known about/open. Most of what I have said is, or should be, obvious. I do feel that things will likely be fixed upon release, and hopefully am right about it.
"I hate to advocate drugs, alcohol, violence, or insanity to anyone, but they've always worked for me." Hunter S. Thompson, A.K.A. Gonzo.