The ferry runs about every 20 minutes. You can also take either the resort or express monorail to the TTC. The trams to the parking lot run almost continuously.
Driving to MK first thing in the morning then jumping on the ferry is a great way to start the day. You can slowly see the castle looming in the distance, there's MK music playing over the sound system, you see all the resorts around you and usually there's a character in a small boat that comes by and waves. To us, it's the best first timer experience - we started our kids that way, too.
Coming back, the walk to the ferry is shorter than the walk to the bus area, and because the trams run so often, it's not a bad experience at all. You just have to expect it to take a little while and enjoy it.