I guess the main issue is that the timeline of events has gone like this:
Snowden/Guardian: NSA is doing X
Govt/NSA: We are not doing X
Snowden/Guardian: Here are some slide/proof
Govt/NSA: Ok we are doing X, but it's for your own good.
Rinse and repeat each fortnight.
So each denial means less and less, and tips believability towards Snowden even where the proof is inconclusive in some cases.
Snowden/Guardian: NSA is doing X Govt/NSA: We are not doing X Snowden/Guardian: Here are some slide/proof Govt/NSA: Ok we are doing X, but it's for your own good.
Rinse and repeat each fortnight.
So each denial means less and less, and tips believability towards Snowden even where the proof is inconclusive in some cases.