I know everyone says Webber doesn't have the car that Seb does, but it still doesn't make sense to me. Spend bazillions of development, not to mention the effective advertising cost of the RBR team with no primary sponsor other than RedBull, pay the driver a small fortune, and then handicap him when actually keeping race wins away from Alonso is probably more important than Vettel winning.
I'm sure the team has been more concerned with helping Vettel this year, but to consciously deny Webber the car with which to dominate the rest of the field during a race would just make no sense at all.
I think ultimately Webber is just not as fast as he used to be, whilst Vettel has improved since his first year at RBR. Webber would be getting similar treatment from any of the other front-runners imo, perhaps even more so from certain drivers.