I agree with this. The limit of 2 is really really low. I have this question here, and in order to prevent the awarded answer from receiving an automatic bounty, I downvoted it. Also, because it really didn't answer my question at all and was thus not useful. But it looks that the answerer got pity upvotes because the guy made an effort, which I would have honoured too, if it wasn't for the automatic bounty he'd get.
So now, the second answer which is going the right direction and might even lead to an accepted answer will never be awarded.
This happened to me every time I set out a bounty on difficult questions. I hardly ever got 100% satisfying answers, because sometimes they are too difficult to answer in 1 week. But the automatic bounty was always awarded to some bounty-hunter.
I think instead of automatically awarding bounties to answers with 2+ upvotes, there should be a vote cast by users with -say- 5000+ reputation, and 5 votes in favor of an answer will award the bounty.
BTW: I set out a
META-BOUNTY for this question, as I think this is really a flaw in the stack-exchange sites :-)