The reason why some people struggle to connect to Gamzee is the same reason people struggled to connect with Anthy Himemiya from Revolutionary Girl Utena in the beginning.
They’re both mysterious characters the narrative refuses to tell you directly about.
Both Gamzee and Anthy are being manipulated by a higher, more powerful figure, who stripped them from any sense of free will and hope for a different fate they had left. In doing so, they hide themselves from the world and simply obey orders, never considering what they want for themselves. That makes it extremely hard to tell what is the character and what is the person behind them ordering them around.
Lord English used Gamzee to bring about his own coming. Akio used Anthy to manipulate Utena so he could come to control her in the end.
They’re both characters who were abused and stripped from their old selves, to come to the only purpose of serving a higher figure. But the narrative doesn’t show you that. At least, not directly. And, in turn, we are stuck not knowing what is the character, what is a product of the person behind or if there even if a Gamzee or an Anthy to begin with.
It’s easy to think they agree with what Akio and LE want them to do and are doing things out of their own accord. But if you know anything about manipulative and abusive relationships, you know it’s not that simple. It’s not simple to leave an abusive relationship, and both Anthy and Gamzee don’t feel like they can leave, they don’t think that’s even an option.
But there’s a key difference between these characters that cements how people see them.
Anthy’s pain is painted on a sympathetic light. Even without directly addressing the issue, it’s clear the narrative does NOT want you to think she deserves the abuse she receives. Gamzee’s pain isn’t.
Homestuck paints Gamzee as someone who deserves the abuse he receives. It paints him as someone who chose the abuse and takes delight in it, as someone who deserves it. And the choice is deliberate.
Homestuck knows how abuse works. Dave’s and Vriska’s abuse is put on a sympathetic light while Gamzee’s isn’t. It’s the core reason why people end up sympathizing for Anthy but not Gamzee. Because Hussie doesn’t want people to sympathize with Gamzee.
For whatever reason that is, the narrative, Hussie wants you to think he deserves all the bad stuff that happens to him. He wants you to think he chose this for himself and therefore must pay in blood and suffering and isolation for it, even though the power imbalance between Lord English and the other characters is made pretty clear.
That’s why people often struggle to sympathize with Gamzee, because Homestuck doesn’t want you to. So while Anthy, even though we don’t understand her, gets a happy ending and gets to leave the abusive relationship she was in,
Gamzee is stuck in the fridge forever. And Homestuck wants you to think he deserves it, even though you have no reason to believe that.
TL;DR: Gamzee is a secretive character we barely know anything about, just like Anthy, but we end up liking Anthy because the narrative paints her as a victim, while Homestuck paints Gamzee as deserving of the abuse he receives.