It is a pain that Uni charge extra for parking (it annoys me no end) but when you think about it it's a fairer way of going about it.
Uni are upfront with their room rates and parking charges, if you have a car you pay parking if you don't have a car then you don't pay parking.
Disney are not so up front with these charges as they will without doubt have factored parking into their room rates, so you will inadvertently be paying for parking. Difference with this system is that you pay for parking whether you have a car or not.
I can kind of understand Univeral's point of view, they're land locked and every acre of room is a prisoner, but Disney have miles of land to use so they shouldn't be charging for parking.
I don't think any hotel should have a parking charge though, to me it's a just a sleazy money grabbing thing to do. It should be included in the price of the room. If you don't drive, you might have to pay more for a service you're not using but it's not like it's costing the hotel any money for you to park compared to you using their free shuttles to the parks.
Looking at hotels recently, I'm also starting to notice more hotels now having a resort fee that I've only ever seen in Vegas and Hawaii.