I would disagree that games are being "fixed" if that is what you are implying. However, I agree that the NFL has been in tough spot in justifying what the refs are doing on the field and in their defense, I would argue that technology and the internet has probably magnified the problems 100 fold.
Sure we could go back to the way games were once played, no reviews, just play ball and the calls all stand as called. The problem with that is technology. Fans would view it as you are now, cheating, collusion, etc. The talk of blown calls for each game would increase dramatically. Anyone with a recording device would have a field day pointing them out and coming up with theories of why the refs blew the call and how it changed the outcome of the game.
Technology and the internet has made "getting it right" paramount to fans. How do you get it right when some of the calls are subjective, plays happen in the blink of an eye, refs vision is blocked, etc? Right now, instant replay is about the best avenue to do that. It isn't perfect and it isn't going to correct every missed call, but if coaches are allowed to challenge calls (any call or non-call) on a limited basis, then at least it comes down to trying to coach out the calls you think are the most critical.
I would never want to see a game where after every play, a call comes from upstairs "#92 was offside, replay the down". However, if a coach wants to use one of his limited challenges on the play, because he feels it was a critical missed call, let him.
We will never see a perfectly refereed game, but at least continue to give referees and coaches the ability to correct the ones that could really matter.