I think there's an aspect that is being missed here.
Disney's goal is to get people to book at their resorts and then to keep them on property throughout their entire stay. If a guest sees Disney as all-inclusive, and never leaves the property, then they are constantly spending money with Disney. If they go off-site to a restaurant, a shopping location, Universal, whatever, then that's money Disney has lost.
Disney's free transportation encourages guests to stay on property. The buses, Skyliner, and monorails all facilitate people being able to stay at a Disney resort without a rental car. If Disney starts charging for those items, more people are likely to make the calculation that they'd rather just get a rental car and drive themselves around property, which then leads to more opportunities to go off property. Disney doesn't want that.
That is actually part of the reasoning behind parking fees at the resorts as well. Yes, of course, part of that is simply about another source of bringing in revenue. But that's actually not all there is to it. It's also so people think "why pay for parking when I could just take Disney's free transportation." Everything they do is very carefully calculated to keep you on property. And even for non-resort guests, if you can hop on the monorail to go from the Magic Kingdom to the Contemporary to have dinner, you may do that. But if there's a fee to do so, you may just go back to your car and decide to go off property for dinner instead of going over to the Contemporary.
For this reason, I find it highly unlikely that Disney will start charging for any of their internal transportation. I think what they would gain would be far offset by what they would lose.
