Because the Brotherhood hasn't exactly proven themselves to be responsible with the use of technology. The East Coast BOS now essentially contains the power of the Enclave, Liberty Prime, Hercules Bradley (if they are able to repair the Mobile Crawler somehow), they use conscription to supplement their numbers, and the Lone wanderer is at their beck and call (and likely very much alive by the time of New Vegas). Then of course if (God forbid) Mothership Zeta is somehow canon, they have a freaking death-ray at their disposal. They could win a war if they went to war and I don't trust them. Its far too much power for one faction.