There was no definitive proof that roethlisberger raped women yet he was still suspended. Greg Hardy was never found guilty of beating the crap out of women but he was still suspended.
This isn't a criminal case, it isn't even civili case, the nfl operates by its own guidelines.
Furthermore Brady hindered the investigation
http://blog.masslive.com/patriots/2015/05/ted_wells_offered_to_let_tom_b.html
"And I want to be crystal clear," Wells continued.
"I told Mr. Brady and his agents that I was willing not to take possession of his phone. I said, 'I don't want to see any private information.' I said, 'You keep the phone. You're the agent. Mr. (Don) Yee, you can look at the phone. You give me documents that are responsive to this investigation and I will take your word that you are giving me what's responsive. And they still refused.
Pats also blocked wells from conducting a second interview with the deflator
http://blog.masslive.com/patriots/2015/05/takeaways_from_ted_wells_confe.html#incart_story_package
Wells provided some context Tuesday, clarifying that NFL security personnel had interviewed Jim McNally three times before he was brought on to investigate the case. Wells only had interviewed McNally once, and he was interested in a follow-up interview.
"The Patriots provided me, in my opinion, with substantial cooperation except in one crucial and critical area: I wanted to do a second interview of Jim McNally," Wells said. "Jim McNally was the second Patriots person I interviewed. I wanted, after interviewing others — including Tom Brady — to do a second interview of Jim McNally, to put some questions to him. And I also discovered after the first interview one of the most important text messages, where Jim McNally not only calls himself 'The Deflator' but says he 'has not gone to ESPN....yet.' Which is akin, as far as I'm concerned, to saying, 'I have not gone to the media yet to report what I'm doing.' And I had not found that text at the time of the first interview. I wanted to confront him with that."
"I asked for a second interview," Wells continued. "I said I would go to New Hampshire (his home). I would interview him in the morning, the afternoon, night — I didn't care. I would make myself available whenever I was free. And not only did (the Patriots) say I couldn't interview him. They said they wouldn't even tell him about my request for an interview. So on that particular point, which was critical to this investigation, they did not cooperate. The report sets that out."
Again this isn't a criminal case. Perception matters. Brady looks guilty and they punished him accordingly.