If I am a tank, I normally call the shots in the flashpoints since if I leave, the group will have to wait for a long time to get a replacement, so if I am short of time, don't need any loot that might drop or just to lazy, I skip bonus. If someone starts complaining I normally just tell them that he is free to leave and find another group, if there is more then one that wants to do it I just tell them to either kick me and do it or finish the current flashpoint without doing the bonus boss. If I am a DPS, I normally just go with whatever the group does be it doing the bonus boss or not, normally people don't do it since the drop is p much crap anyway.
If you're so short on time that a bonus boss would kill your scedule you might shouldn't run any FPs ... just an idea.
To the topic:
If anyone needs the possible loot, or majority agrees on doing bonus I do it, no matter if I tank, heal or dps. Of course it is easier to go for bonus while I tank :P