This is to limit the number of bounty questions in the system (i.e., to continue giving them special attention). If there are too many bounty questions, they aren't special anymore.
Under the new system, every single question in the system is now eligible for a bounty by anyone, instead of only the user's own questions, and every question can have a bounty added repeatedly. This is a HUGE increase in the potential number of bounty questions that could pop up, so they had to be limited somehow.
This is also an equalizer of sorts between high- and low-rep users (unknown if this was intended or not). While I agree that high-rep users should have more abilities in the system, limiting the number of bounty questions lets the low-rep user's question get better attention since it won't be dominated by many many more bounty questions set up by high-rep users. High-rep users already have a huge advantage of being able to set up larger bounties without as big a relative penalty (think of a 50k user and a 1k user setting up a question with a +500 bounty on it). The value of the question with a bounty on it isn't really related to the reputations of the users involved anyway.
So, I disagree with the proposed feature request as stated. I think it could possibly be increased to 2 questions at once, but it would be a good idea to first give the new system time to stabilize to see how many people actually take advantage of the new ability.