It's the size that's the cause of the problem. When you have a guy who can beat triple coverage reliably, when there's no legal way to defend against what he can do to a defense, the refs are GOING to let ticky tack stuff go on that player.
They do need to get better about calling clear violations of course, but what you don't want as a ref is defenders getting so frustrated about not being able to cover Gronk within the rules that they take the law into their own hands and start going for the knees. So you let them have the gray area stuff to give them some kind of outlet short of wiping out a player's season.
It's a lesser of two evils thing, it's not OK, but as an NFL fan you kind of have to accept and deal with the fact that it needs to happen with certain players. Gronk is one I know it happens to, Travis Kelce is another, and neither of them like it very much but I think they'd like the alternative even less. I know Gronk's had his knees targeted more than once as it is, if defenses start thinking it's the only way he's going to get stopped... well, teams want to win games don't they?