I think it's a lot of factors, none of which are to make people pay for a cab to drive off property, or to have them stay off property, or to deter terrorists, or some of the other reasons stated above.
Some factors:
There was pressure by other religious groups to be able to offer services at WDW. Some of these groups are not "mainstream", and WDW was in a bit of a pickle. They didn't want to be called discriminatory, but they also didn't want certain factions tearing into them for "Supporting" non mainstream religious beliefs. They were basically forced to cancel all services. IMHO the biggest screamers about the non mainstream groups would have been the two groups who were already getting services. So WDW was in a no win situation.
The early Catholic mass didn't have huge attendance numbers. If you didn't have a car it was hard to get there. They had started to run "Church busses" from the resorts directly to the Poly on Sunday mornings, but that was costing money. I have no problem with Disney not wanting to spend the money on this. Fewer than .01% of the guests used the service, yet the cost had to be passed on to all.
The Protestant mass didn't do big numbers either.
There was some cost to WDW associated with offering the services, including clean up of the facility after the mass. Again, this cost had to be passed on to all guests for teh convenience of a very few.
Anne