Let me clarify...
When you get out of a BG you are still flagged for 5 minutes whether you want to or not. This makes you susceptible to an attack from another player, even though you didn't flag yourself. This happens on both a PvE and a PvP server.
I don't know about your server, but on mine (thanks to CRZ ) there are at times 1-3 rogues just waited for lowbies to get out of BGs so they can ambush, cloak, and vanish... then repeat. Hell, today I saw a fresh 90 do it in green gear! I even saw an 85!
This has to stop, especially on PvE servers.
The obvious solution would be to have the game not flag the player after a BG on PvE servers, PvP servers I think can stay the same because it was your choice to be flagged all the time.
That's just my idea though, got any others?