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The former Chelsea, Real Madrid and Manchester United boss has put Roma in the mix for a top-four finish and a place in next season's Champions League, yet he feels he continues to get a raw deal.
Goals from Roger Ibanez and Tammy Abraham inside the opening six minutes set up the latest victory that moved the capital club, at least briefly, up to third place in Serie A.
Mourinho is thought to have been wanted by Portugal after the World Cup but the 60-year-old elected to stay with Roma and hopes that will prove a wise decision.
A narrow defeat to runaway leader Napoli last week was followed by the blow of a shock Coppa Italia quarter-final exit at the hands of Cremonese, which is rock bottom of the Italian top flight this season and yet to win in the league.
Roma fans booed at times against Empoli as they continue to reel from that cup disappointment, with captain Lorenzo Pellegrini not spared when he came off in stoppage time, near the end of the game.
"Pellegrini has a coach who respects him and respects everything he does for the team. Out of 60,000 people, maybe 20, 30, 50 people boo," Mourinho said.
He said his team was playing "with our limitations", a reference to its limited squad depth, and said beating Empoli should be regarded as "an excellent victory, because we played against a very difficult team".
"Some fans don't understand it but this is normal," Mourinho said.
"Fans love the club but football is not their area.
"Obviously there are those who understand and there are people in the press who should have understood, because it's their job, and who in my opinion understand but pretend not to understand that this is our reality."
For the Cremonese cup game, Mourinho started without a number of his Serie A regulars, believing they needed to be protected from a heavy schedule, but the likes of Abraham, Nemanja Matic and Paulo Dybala were back in the starting XI to face Empoli.
"I think that if this team plays against Cremonese, we win and we're in the semi-final of the Coppa Italia," Mourinho said.
"But then we wouldn't have won today. This is our reality. We always do our best, we work hard.
"Today, before the game, I told the players that we have to go onto the pitch with a backpack full of the frustration and sadness of the last game, but we can't expect anyone to help. Just us.
"For the first time I went on the pitch with them in the warm-up and our feeling was exactly this: it's just us.
"The truth is that we do our best. And as I always say, when you give your best, you can't give more. We always give our best.
"I think day after day. I could have left in December and I didn't leave, I stayed here.
"And this is my life.
"Sometimes it seems like we're in trouble, in the relegation zone, but we're there, we're at the top, with all those teams that are very strong. But that's okay."
It remains uncertain whether Mourinho will be in charge next season, and whether Nicolo Zaniolo and Chris Smalling will stay at Roma.
Attacking midfielder Zaniolo had a January move fail to come off, after he appeared to push for a transfer before hesitating when Bournemouth appeared to be his likely destination.
Former Manchester United and England centre-back Smalling, who started against Empoli, is nearing the end of his contract and reports have claimed Inter and Juventus are keen on him.
Asked what Zaniolo had to do to be welcomed back into the squad, and how Smalling might be persuaded to stay with Roma, Mourinho said: "Zaniolo must do absolutely nothing, it is a problem of the club and he must solve it with the club, not with me.
"For Smalling I can do nothing to convince him."
