Is a bit different than that. They are complaining now because the revelation of this is making their paid users to stop using their services. They may or may not be worried about their users privacy, but for sure they are worried about their profits.
In the other hand, tif well they knew the cut of the cake they were getting, they didn't know about all the other companies into the same and how wide and deep were this. Also, the revelation on how the NSA infiltrated their internal network without their knowledge or consent could had raised some alarms.
In any case, if the NSA head can lie to the congress without consequences after that being found out, why can't they tell all of them that it is over while keep doing it (and keeping the backdoors in their internal networks to keep doing the dirty work) or force them in a way or another to tell the world that all is over when is not, or even plant a fake whiteblower that confirms that the NSA stopped their programs ? By now trust is deeply broken in all that surrounds the NSA, if tomorrow they say that 2+2=4 you should bet that they are doing math in base 3.