I don't disagree that it's EASIER to take a minivan to the garage and park there, but how many of these suburban families making a day trip do you think only go to the aquarium? They walk over to Quincy Market, maybe the Common, and do other things, they literally, "make a day of it." As a result, the parents are prepared to be walking with their kids everywhere and they know their children's limits; they know when they get tired, they know when they can't carry their own stuff, they know how far their kids will wander off.
If these are day trips during the week, it's usually a group of soccer moms taking their pre-kindergarten kids as a group (4-5 kids per 2 adults) if it's weekend trips, it'll be elementary school kids with mom and dad (2-3, maybe 4 kids per 2 adults). I know this because this is what my family and our family friends all did when we were younger. The train is a fun adventerous trip for the kids. It's not as bad as people are making it seem either as the train is relatively empty on weekends and kids can only go so far on a train car.
Again, yes it's easier to drive, but it's not a killer task to take the commuter rail in for a day at the aquarium, you only have to be a moderately alert parent and it'll be a relatively easy day. I did one of these trips with my girlfriend and her 6 and 9 year old brother and sister a year ago and it wasn't hard at all.
Worst case, if they want to drive so bad they'll park at another nearby garage, it's not like it's an impossibly far walk from any other garage. I think we're going overboard in saying that attendance at the museum will take a major hit if the garage is taken down. The aquarium is it's own worst enemy, not parking.