Messi was one of the players PSG fans took out their frustrations on when the club was eliminated from the UEFA Champions League by Real Madrid.
The former Barcelona forward was jeered together with Neymar despite a 3-0 win over Bordeaux in the aftermath of their European elimination.
In a difficult first season in France, Messi has only scored two goals in 18 Ligue 1 appearances but PSG are well placed to reclaim the title from Lille.
Fabregas feels criticism of his former Barcelona teammate is unjustified and the PSG fans should rather enjoy the seven-time Ballon D'or winner.
"Leo's case is very simple. For me, he has been the best ever that I have seen and played with. What I have seen from him has been exceptional," Fabregas told Marca.
"I know what happened with PSG. The fans want to create a moment of tension with the players.
"During the match, they support you; when they sing your name, perfect. But what I saw the other day – jeering when Neymar lost the ball or whistling when they touched the ball – is very ugly.
"They justify that they get paid a lot. They lost against Real Madrid – that's fine – but didn't they want to win? That's what comes first.
"With PSG, they haven't won anything yet, for the moment, but they will surely win the league.
"You're talking about a player [Messi] who has just arrived. PSG have never had a player like this in their lives.
"It's better to be grateful, to support him and not crush him. This year or next, these guys will bring you great moments."
