Ensemble Dark Horse: Yuu is far and away the most popular of the Sanrio Boys, due to his backstory, his ability to open up to people, and his caring for his sister despite her irritation with his personality. On one of the official polls, he was first, and despite Kouta being billed as the first character, the first romance character-centric manga arc featured him.
Despite the message of the series being to understand and come to love characters that wear their Pink on their sleeve, the Periphery Demographic of the franchise is the exact same people the series is about, meaning they were an afterthought to a project explicitly about people like them.
On a more humorous note, the boys themselves have Sanrio merchandise like their favorite characters. Time will tell if a boy shows up in-universe that fanboys them too.
Some Anvils Need to Be Dropped: You shouldn't be looked at funny for the things you like, no matter what they are. And boys should be allowed to like things typically seen as "girly" or immature.
Spiritual Adaptation: Some folks have called the series the 2010s answer to Otomen, a similarly themed shoujo series about boys learning to embrace their feminine hobbies.
For the anime:
Accidental Aesop: With how easy it was for Yuu and Shunsuke to express their Sanrio love in episode 2, some people ended up seeing the message as "If you're already popular with girls, they're not going to care if you have a couple of quirks".
Ryo turned out to be the least accepted of the boys in the adaptation, due to his unsavory attitude towards everyone save for Seiichirou and feeling like he acts "too" girly in a bad way (referring to his perceived cattiness and flippant attitude) despite wanting to be more masculine. His portrayals in other media went better, but here he's not well liked.
Seiichirou doesn't have as many fans in the anime despite his popularity elsewhere. He's appreciated for having his life together as well as not needing a reason to like Cinnamoroll beyond seeing him as an escape from his stressful life, but the lack of focus on him in the series makes him look too perfect in the eyes of some fans and they consider him bland as a result.
Ending Fatigue: The anime becoming drama focused in the latter half of the show caused some fans to drop it, considering that despite some sad moments in the first half it was still largely a fluffy slice of life anime.
Genius Bonus: Seiichirou joins the main cast by trying to mediate between Ryou and the other boys, he earns Ryou's respect by sticking up for him against other students, and he always watches out for weaker students and tries to keep them safe. Cinnamoroll's official Twitter page has been the target of trolls for years who send crude edits of official art and harassing messages to every post, no matter how many of them Sanrio blocks. No wonder his biggest fan would be so concerned with bullying.
LGBT Fanbase: The series' premise has seemingly started to slowly attract transgender viewers.
Narm: With all the heartfelt scenes, drama, and blatant Fanservice paired with the super-cute visuals of Sanrio's greats, the overall effect of the show can be quite jarring at times.
They Wasted a Perfectly Good Character: The yumejoshi fanbase of the series were upset to find out that the visual novel protagonist and the girls in the manga adaptations won't be showing up in the anime, and felt that their dynamics with the characters would be fun to watch in an animated format.
Wangst: Ryou's problems with his femininity reads like this to some Western fans. The fact that he doesn't get bullied for his looks and has the attention of some of the most attractive students in school, yet still wants to become more masculine and "throw away" his connections, doesn't mesh well with this group. Regardless of his fears of the love he gets being patronizing, this party argues his problem is less about hating who he is and more learning to accept himself and take advantage of his popularity, leading to some Unfortunate Implications that he'd only continue to be accepted if he stayed feminine.
Kouta. He has always loved the cute Pompompurin his loving grandma gave to him, only for the other kids to start to mock him over it. When his grandma tried to give him some emotional support, he loudly rejected her, but ultimately got struck with guilt over yelling at her. Just when he was about to finally apologize to her, she died. Since that day, he has been struggling with his internal insecurities, something that has made his life incredibly hollow.
Yuu, due to his dreadful relationship with his younger sister and the burden of all the responsibilities he had to take since their parents are hardly ever at home.
Shunsuke, as he was shown to have a deep-seated fear of bonding with other people out of fear that he'd suddenly just lose them some day, like how the little girl he was fond of in childhood moved away soon after he bonded with her, the two never meeting again.