Their attendance seems nice at face value, but the Mallards benefit by only playing during summer and not having to sell tickets to April/May games or to games after school is back in session. Going to a AAA game and going to a Mallards game are very different things. Ticket prices alone are 2x as expensive in many seating areas/cases. Instead of convincing someone season tickets are $375 for a nice seat behind homeplate, they are $1,300 a seat. I am sure prices are vastly different in many other cases too. I would also venture to guess the facilities are way under MiLB AAA standards.
A lot of teams have 3,500 AAA attendance, but it is simply because someone invested the money to have a properly sized stadium and good enough facilities. From an attendance standpoint there are plenty of great locations, many probably way better than Madison, if they were willing to invest the money to keep up with MLBs ridiculous standards. Trying to keep up with MLBs demands and have an organization profitable enough for all those costs is pretty hard to do.
But it is kind of a moot point due to the contracts for MiLB teams. A team would have to move to Madison and it wouldn't be our current affiliate as the current affiliate has some of the better attendance in MiLB. The Brewers would likely have to buy the AAA team and then basically build an entirely new stadium...all to just poach off of the MLB team for fans/attendance.