I mean seriously, you go out and assault an air force base, for what? Nothing but to destroy that huge badass mobile base with orbital bombardment satellite uplinks, using itself. I mean you could also bomb the Pentagon, but seriously?
Why would the Brotherhood, of all people. order the destruction of such a fabulous piece of technology? Why not have their hero go and clear the base first then send in their own force behind him to capture the base, vertibird hangers and radio control tower? I mean having all those vertibirds, that left over Enclave tech after their slaughter, that huge communication tower, a mobile base crawler and the ability to call in orbital bombardment couldn't possibly be a bad thing, especially with the recent loss of Liberty Prime. You'd think they'd want ownership of the only thing that's a bad enough dude to stop that giant metal patriot.