Yep, they want people to not have cars - for a few reasons.
More cars means more accidents. Since Disney has a lot of buses on those roads, more private cars increases the chances that their buses will be in an accident - increasing their legal liability.
More cars means more drunk drivers. The headline "family of four killed by drunk driver while on vacation at Disney" probably keeps PR people awake at night.
More cars means more security holes. While anyone intending nefarious purposes isn't going to be stopped by a parking fee, fewer cars means fewer guns in gloveboxes on site for an opportunistic rage shooting.
Cars give you a way offsite. Disney would like you not to go to Universal or eat offsite. They'd rather have you do your souvenir shopping onsite than at the outlet mall.
Universal has been charging for parking at their hotels since opening. It hasn't stopped people from going to Universal. Its a good bet that there will be some outrage, perhaps a short term attendance blip, and then things back to normal.
At some resorts, parking is at capacity. They either need to reduce usage or add capacity. Adding capacity is an expense, and parking lots aren't attractive. Reducing usage make far more sense.
And as an added benefit to Disney's bottom line "parking is included in your DVC membership" will now be part of the sales pitch.