Because the rule is the rule and the exception to the rule is only applicable if the driver sets a good enough time in one of the sessions (usually FP3 because FP1 and 2 are typically slower). Im not certain about this case but I dont think that D'Ambrosio set a time in FP3 that would have qualified him in the rule, and I am pretty sure that that is the benchmark.
Personally I never rated Alonso as a driver. Im not trying to incite a war here but taking Massa out of the equation so it doesnt become a "who is better than who" argument, which is entirely subjective. When Alonso won one of his championships (I think the second one) he got lucky when Schumachers engine blew up in one of the last few races of the season which pretty much handed it to Alonso. That year he won the Singapore GP in the Renault it was down to bad luck for I think Massa who was leading and then a pitstop error (IIRC), and of course there was the big scandal about Piquet. So essentially he cheated his way to that win. (Or at least Renault did). When he won the Bahrain GP last year (someone was saying that they had a better start to last season than this one) he also only won that race because of a spark plug failure for Vettel.
Obviously there are races that he won on out and out skill but he certainly has a lot of luck on his side and inherits a lot of wins.
Now ignoring Alonso, Massa is doing great for a driver in his position (or anyone for that matter). I mean the guy was in a freakin coma. (personally) I dont know anyone who has been in a coma, and in wider publications I cant think of anyone who has been in a coma to come back and do anything as mentally draining as driving an F1 car. Or even do anything for that matter.