Wigan Athletic boss addresses Kal Naismith booing
But he acknowledges the only way to silence the knockers is for his side to get back to winning ways - starting this weekend at Luton.
Naismith was jeered by a section of his own fanbase when he entered the fray during the second half of last weekend's 3-1 home defeat to Reading.
Cook was also given the treatment in the last 10 minutes, and the Latics boss has appealed the supporters to think about their actions.
"I think as a manager and a player, you have to be very careful about which fights you get involved in," he said.
"Wigan Athletic fans - like most fans - can make up their own minds about what's going on.
"Because if you're paying your money into a football stadium, the reality is you are entitled to your opinion.
"Just because my opinion might not be the same as that, or anyone else's...the reality is football has gone that way.
"Do I agree with it? No, not at all.
"But is it the supporter's prerogative to do that? That's for the supporters to decide."
When asked specifically about Naismith, Cook went even further in defence of his player.
"If I'm a Wigan fan, I'd be looking at myself and asking if that is the correct thing to do," he said.
"Do we want to send our players on the pitch like that?
"It's not my debate, and I'm not getting involved in it.
"Football is a brutal game at times - for managers and also players.
"But I just think sometimes you've got to be careful how far you go and how quickly you go there.
"His negative chanting is...will it change?
"I'm not so sure...you've only got to look around football.
"But is booing your own players as they're coming on the pitch the correct thing to do?
"I would stand up and demand 'no'. It's not.
"I think it's an absolute disgrace, it's a travesty.
"Will that stop it? I'm not so sure it will.
"Will us winning football matches stop it? Of course it will.
"So let's concentrate on what we can try and control."
Social media and message boards have also been dangerous places for Cook and his players of late.
But the Latics boss says that does cause him any additional anguish.
"I don't have no interest in social media," he added.
"I don't look at it, thanks goodness - because I can only imagine what it's like.
"I'd be very interested to see who they'd like as the next manager, though, that would be interesting!
"But that's not for me, is it?
"I think everyone can see what's going on in the managerial world these days.
"I've been a big advocate of Talksport, and all they're doing these days is discussing managers - who are still in work - being sacked, and who's going to go in.
"I think that's very, very sad for football, but that's just my opinion."