But the problem I see is on most cases the whistle doesn't even blow until the play is over or the ball is in the air, IMO that is too late and they shouldn't over turn it, they should just say tough crap, you should have called the TO quicker Coach.

Look at it this way then, no kickers involved. Say you are driving on someone and down to the 5 you snap the ball and hit a quick slant over the middle and bam GW TD.........not hold on, a whistle has blown (late) after the play has already happened and the ref comes up and says the opposing Coach called a timeout. How do you really know they did, you didn't blow a whistle until the play was either over or the ball was in the air. Would it be fair to make the team try it again from the 5 because they called the timeout too late.

That is the problem I see, the refs wait too long to call the timeouts and the ball is already up. Tough crap to the opposing team who called the TO, you were too late. But that is not the way it works, they grant them the TO and have to kick it again. It doesn't bother me that they do it, it is just the timing in which they do.