I think he actually made a remarkably positive comeback from his accident performing very well.
Really?
Before Germany, we would routinely see Alonso qualify behind Massa. Then watch Alonso cruise up behind Massa and get stuck behind him.
In Monaco I think Alonso started from the back of the grid and then cruised up behind Massa. And this was at Monaco of all places.
Germany was another instance of Massa being in front of Alonso, then Alonso cruising up behind Massa.
Germany wouldn't effect his confidence, but it would've made clear to Massa that Alonso was now the daddy at Ferrari.
This year, Ferrari have arguably the most difficult car to drive, on the grid and what you are seeing is Alonso showing just what he is able to do. Massa is trying, but the car is horrendously difficult. Hamilton could probably hustle in this year's Ferrari, but even somebody of Button's calibre would struggle (as he requires the car to be well balanced). Do remember that in qualifying, Massa was only 0.3s behind Alonso, which is what you would expect from a No.2 driver, so Massa did an OK job in qualifying.
It's a little unfair that Massa has Alonso as his team-mate. If he had Kimi, he probably wouldn't look so bad, but against Alonso, most drivers (even the good ones), would look ordinary and would therefore come under fire from the Italian media.