The NFL does not pick up a newspaper, see that there was an allegation, and dole out a suspension. They do a careful investigation of the facts.
You cannot stand up at a microphone, say Chris Johnson shot your foot, and see him suspended shortly thereafter. The NFL would gather all of the evidence, meet with Johnson, get the statements of any witnesses, etc. Roethlisberger's case didn't go to trial but there is a tremendous amount of information available.
The NFL cannot wait on legal verdicts because law enforcement and prosecution is a local, flawed, inconsistent process. I think you can debate whether it is fair to punish someone without a guilty verdict, but I can certainly see the NFL's logic. Rapists are bad for its image, bad for the product, bad for revenues. As are unconvicted assumed-to-be rapists.