Even with the free motorcycle fare, the ferry is still incredibly expensive for supposed time savings. Unless your schedule mandates you go through Chicago at rush hour, you can get to Milwaukee from Muskegon in 4.5 hours. The ferry is a 2.5 hour ride plus an extra hour by the time you board, load, and unload.
I've got the best excuse to take it since the ferry is only about 2 miles from my house. I've been on it a couple times. It is one of those things that sounds like a great idea until you actually run the numbers so I don't in most circumstances. But there are intangibles that I don't necessarily place value on. To me, travel time is travel time no matter if I'm sitting, sleeping, or driving. Chicago driving doesn't phase me but I can understand why people want to avoid it. It is a smooth ride usually and a neat experience if you haven't done it before. I take Lake Michigan for granted because I've lived here for so long.
If you're going to do it, free motorcycle fare is the time to do it.