The Bleach anime isn't exactly a great example for people to use as a reference when it comes to ships, since it's common knowledge that the anime director really liked Rukia and favored her in several ways that the manga never did.
Firstly, in the manga, Rukia has much more of an older sister (onee-san) role to Ichigo than a friend or even best friend. Rukia's best friend is actually Orihime. The two women build this kind of friendship. As the story develops, Rukia becomes a kind of mentor to Ichigo.
Rukia couldn't have a romance with a 15-year-old boy like Ichigo, because she already had an emotional history with Renji even before Isshin thought about going to the human world. We're talking about decades, centuries of this relationship here (It's in the manga that Rukia didn't even want to be adopted by the Kuchikis and she waited for Renji to stop her from leaving).
When Rukia and Ichigo meet, Ichigo already knows Orihime and has a teenage crush on her (the boy says in the early chapters that for her brother to attack her, he'll have to kill him first).
After Rukia goes through the Soul Society arc and reconciles with Renji, she starts spending more time with him and the other Soul Reapers. Ichigo has his group (Orihime, Sado, and Ishida), and Rukia has hers. She only returns to the human world for a mission and goes back with the other members of the Soul Society.
In the manga, the story revolves much more around Ichigo and his group than the Soul Society members. Rukia and Renji are occasional members of Ichigo's group.
You can see this in Ichigo's reaction between Rukia's imprisonment and Orihime's kidnapping. Rukia's imprisonment was a much greater emotional burden for Renji, and Ichigo only went there (with his group) because Orihime encouraged him. And because he felt guilty that she was imprisoned "because of him." In the Hueco Mundo arc, it was an emotional burden for Ichigo, and he goes alone to rescue Orihime of his own free will, alone, without his group. His group follows him.
It's in this Hueco Mundo arc that it becomes evident in his fights against Grimmjow and Ulquiorra how much Orihime affects even his will to live (Vasto Lorde).
These are very different and much deeper developments from the anime.
Orihime's haters hate her and prefer Rukia with Ichigo solely because, at the beginning, she was a very passionate and vulnerable girl. It's impossible to compare an ancient, centuries-old soul like Rukia with a 15-year-old human girl who had no family and was abused her entire childhood. Why does vulnerability scare you so much?
Renji makes sense for Rukia, and Orihime makes sense for Ichigo. The manga already started with these relationships established. Kubo didn't deceive anyone; you created an expectation that never existed based on an anime with a lot of things cut, changed, and many fillers. Kubo has already expressed a desire for a reboot of the anime that is much more faithful to the manga.
