Could always do planetary content.
When I play through the storylines, I don't want to be interrupted. At all.
So when I know a flashpoint could pop at any moment, I like to do something that isn't story-heavy. The only real options, then, are Space Combat and PvP. I'm bored of Space Combat, so the choice is PvP.
Why would they prevent people from queuing for both? This is going to make the people who prefer Flashpoints ONLY do flashpoints and no pvp, and vice versa - which means people will get bored sooner from doing the same thing over and over (or in the case of flashpoints, waiting around doing nothing for ridiculous lengths of time).
For level 50 content, I somewhat understand it. For level 10-49? It just doesn't make any sense. Flashpoint queues take forever for lowbies, even on populated servers. Who cares of people leave a warzone from time to time in lowbie PvP, anyway? Someone else will join to fill the slot.