The cost of a parking space is actually quite high. In 2002, the average cost per stall was ~$3000 per stall, above ground structure $15,000 and underground ~$27,000. Using nominal inflation, that would be ~$4,000 a stall today, using actual inflation limited to the construction industry it is likely quite a bit more. I know that for a project we just did here in Canada it was easily double that.
Add in the annual cost of the service of probably around ~$750 and costs add up quick. A parking stall at $14 per day has to be used a minimum of 50 days a year to simply recoup operation costs without considering capital at all.
For more info see here:
http://www.vtpi.org/tca/tca0504.pdf
Parking lots aren't cheap to operate, and I as a guest who stays at a Disney Resort and uses Magical Express would rather see my Park Hopper fees go towards the park vs subsidizing someone else's parking. This also can encourage transit usage which is good from a environmental perspective as well.
Finally, the parking fees are probably the last piece of a transportation puzzle designed to get people to stay in WDW Resorts. On a 7-day (in Park) trip, one can save$98 dollars in parking, add in the free Magical Express, and one saves $66 for 2 PAX instead over using a shuttle, or even more if one had originally planned on renting a car or taking a taxi.
This ~$150 savings for 2 PAX would be enough to make me want to stay at a WDW Resort Hotel. If I had kids, or a larger party, the savings would be even more on the shuttle. This doesn't even consider the added convenience of using Disney's transportation methods, such as the resort->park buses, monorails, or boats. The vacation time saved by simply stepping out of the lobby and into a bus or a monorail is almost priceless to me.
In closing, I agree that parking fees are necessary to prevent a leaching of Park ticket fees going towards subsidizing parking, and from Disney's perspective if parking fees help get more guests to stay in their resorts, parking fees are even more valuable.