Most hotels with parking shortages will charge for parking. It is not limited to NYC or Chicago. Many other Orlando hotels do the same thing. Disney has a ton of space to be able to have free parking. Swan and Dolphin have no space and they charge.
The charge is there to try and discourage you from having a car. If you are changing your mind about a rental car, then the charge has done its job.
There is a ton of parking at the parks, so that would be why that cost is lower. Once you get to the hotels, you will see why parking is a premium. Universal hotels are located right in the middle of an area where they cannot stretch out. There just isn't any more space. Although they are in central Florida, they are also squashed into an area surrounded by highways, houses, high schools and other hotels.
Some people seem to think that jacking up the prices to hide the parking fee would be a good idea but others like the fact that if they don't park, they don't pay.
Universal hotels are great value even with the parking fee. All of the deluxe hotels at Disney are more than $12/night more expensive than the Universal hotels.
Have a great vacation and try not to let it bother you. Focus on all the extras you are getting without having to pay for them, like the express passes.