Looking through the results I think Webber has been ahead of Alonso 5 or 6 times. What I mean by costing him points is just that he's been ahead of him (obviously the main one being at Silverstone when he passed Alonso for the lead with only a couple of laps to go). I don't think there has been a single instance where Massa has taken points away from Vettel by finishing ahead of him on the track.
Ah, that's how you ment it. Well, by the same logic then, Webber took a lot of points away from Vettel too - as underlined by his 2 wins. As I said, if RedBull had put as much support into Vettel as Ferrari is giving Alonso, we wouldn't be having this discussion as the championship would be well wrapped up. Instead, the whole world would be crying foul-play by the dominant redbull. To hear voices that think it's fair that Ferrari does it only because they are the supposed underdog just reaks of hypocrisy.
About the legality and spirit of the rules thing - it's happening everywhere. Vettel being able to set up his car for straight line speed in the race after being DSQ during qualifying in Abu Dhabi is a technicality as well.
That's hardly comparable. Maybe you would have thought Vettel not taking part in the GP at all to be fairer - because that's how much difference it would have made if he had not been able to make crucial set-up changes.
What people fail to see, is that RedBull had a front-running car and they set-up their car for that in qualifying - good traction, more downforce, less straightline speed. They made an error - they were disqualified from qualifying. Now, they had to start from the back of the grid with a car set-up for traction but not straightline speed. If they had started the race like this, Vettel wouldn't have made up many places because he would have hardly got past many cars in the DRS zone. To solve that - they took another penality for changing stuff on the car and had to start from the pitlane.
Starting from the pitlane is a higher inconvinience than you think. If it weren't, then more teams would do it. RedBull had nothing to lose and they gave up the advantage of starting with the rest in order to change things on the car. What they did is within the rules (yes, even within the spirit of the rules) because it allows them just like everyone else to make changes to the car under park-ferme, but they then have to start from the pits. RedBull wasn't the first to do this btw.
This is a little bit different to Ferrari taking a bogus penality in order to get one of their drivers a clear advantage while also affected other drivers on the grid.