These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Broken Base — Purposefully invoked by having star character Franco Rivera "come out" as a a Firefighter For 9/11 Truth who points out how various policy-makers spoke of a "new Pearl Harbor" as the first step toward an American-dominated world. These views are shared by his actor, Daniel Sunjata.
Jerry Reilly also counts as a Creator's Pet, especially when you consider that most of seasons one and two focused upon him. It was only when they begun phasing him out (season three) that a slew of characters (most notably Garrity and Lou) began to finally get screentime and character development.
God, where to begin? Well, Tommy raping his "ex-wife", then calmly talking about dividing the furniture, the frequent sexual scenes of the firefighters, and the very graphic alcohol abuse that takes place.
How about when Lou cuts a cockring off Franco with power tools?
He Really Can Act: Adam Ferrara, a stand-up comic who was part of Leary's entourage, as Needles.
Moral Event Horizon — Rescue Me is a show about some seriously flawed individuals, so there are several which might qualify. But the biggest two come in season three, when Tommy rapes his wife Janet during a private meeting to discuss their divorce and several episodes later, Sheila (unaware that Tommy had raped his wife, but pissed off that Tommy had been seen in public with his brother's ex-wife) began a campaign of raping Tommy via date rape drugs and covering her tracks by way of making him think that he fell Off The Wagon and blacked out after wrecking the apartment. Things culminated in her drugging him and raping him and ultimately accidentally burning her house down and nearly getting both of them killed.
Besides the rape, she also faked being pregnant, tried to force Tommy into selling his and Janet's newborn son to her, and openly opined to Tommy that she would have killed him if he had not made a speedy recovery after being shot by his uncle.
Mike crossed several of them early in the series. In season two, when his slightly overweight girlfriend dumps him (largely because she was offended when he began encouraging her to be bulimic), he goes all crazy stalker on her, brandishing a gun and telling her that she will never ever find a guy as good as Mike due to her being "fat". Similarly, in season three Mikey exploits a gay man he had a crush on for free oral sex and and a place to stay, while outright refuses to provide his boyfriend similar sexual favors. When called out on his selfishness and being a user, the two beat the crap out of each other.
Seasonal Rot: The second half of season five (which ran for 22 uninterrupted episodes) is disliked for fans, due to them introducing a new female fire fighter for Tommy to lust after on top of Sheila and Janet, as well as the pandering to Mike Lombardi as far as writing his IRL band into the show for a crappy arc.
The Woobie — There are times when Sheila gets so caught up in all the drama and she just doesn't have the maturity to deal with it all...it's honestly very sad. Not that she's the only one. When Lou lost everything to the prostitute, when Franco lost his daughter, when Tommy loses ANYONE, watching Jerry deal with his wife, when Sean learns the truth of his sickness, etc. It's just a big Woobie show.
Garrity gets extra woobieness given the fact that the show has repeatedly shown that he's a truly nice (if dumb) guy who behaves like an asshole simply due to peer pressure, from his asshole siblings, cousins, and coworkers. The only other character who doesn't seem to have the same inherent asshole nature to him is Lou and even he succumbs to it in season three after being bilked of all of his money by a con artist.
Sheila's woobiness is further solidified at the end of season six and through season seven by her destructive antics being toned down and her son Damion having his accident on the job, leaving her as his sole caretaker while she can't accept that he probably won't recover.