Presumably if the President decides to pardon someone, as opposed to commuting their sentence, it's indicative of a feeling that they shouldn't have been prosecuted or punished in the first place. So there's at least some reason to question whether they're really criminals or not, particularly if they haven't been tried and convicted of anything before receiving a pardon.

Commutation of sentences is actually much more common, particularly at the state level, because it doesn't really carry with it any indication that the person didn't commit a criminal act (and thus is less politically risky), only that the punishment was either too severe or that there's no reason to continue with it. I believe it also doesn't block further civil penalties or suits, although I'm not clear whether a Presidential pardon actually does (haven't ever seen any examples of that).