While football is obviously a violent sport and injuries are part of the game, putting bounties on other players will cause injuries to happen which might not have happened otherwise. Just one example that comes to mind: a unsuspecting QB is about to get sacked. The linebacker who knows he has a guaranteed tackle might ease up a bit knowing he has the sack no matter what. The linebacker looking for a bounty might try to kill the QB even though he doesn't need to, just to injure him for the cash.
Sure, the bounties were small enough that it probably wasn't that huge of an incentive, but if a message wasn't sent by the NFL, bouties could have gotten out of hand. Espcially if they started working well.