A thing that I notice reading the comments is that a uke raping the seme is more accepted ...

I felt the same way. Looks like most people are fine with rape when its against a man who's penetrating but if it's a guy being penetrated everyone is gonna comment about it and not be okay with it. Double standards...

An interesting observation.
If I had to guess, I'd say it might have to do with the fact that most yaoi forces the reader to view the story from the uke's perspective. The uke is usually the main character and often the more feminine character. As most yaoi readers are female, they are going to gravitate to relating with the uke. Another thing about yaoi is most of readers are probably reading it so they can fantasize about getting fucked by a hot guy. So the readers have already "consented" to any sex that happens because they are viewing themselves as the uke that's getting fucked. So even if they uke hasn't really consented the reader has, and even if the uke is incapacitated the reader isn't, so it doesn't "feel" like rape from the reader perspective. You have to actually take a step back and read it like a story, not a fantasy fulfillment device, to see what the situation really is to see the rape happening. It could also be because people don't want to imagine themselves being raped so they tell themselves it's consensual and reject any suggestion otherwise. Another possibility could be that people doesn't want to admit they have a rape fetish and thus argue it's not rape.
On the other side, when the uke does the raping it might be easier to see as people like to see themselves as good person. This means that when the uke does something as wrong as rape people are unable to relate and call it out.
This is all speculation, don't treat it as fact. I just think this is an interesting topic to speculate about.

No, uke raping the sème is not okay. But here given the context, Ian was locked in a room and abused physically and sexually for years. He probably don't really know what personal sexual boundaries are.

Yeah I understand, and you are right that the background and context of the character should count, not as a justification, but at least it gives them a reason as to why they act that way even in their wrongs.
Here not only the background of the character but even the time the story take place, I don't believe that at that time there were any talks or concerns about human rights, much less rape.
But at the same time thats not what I am talking about, I am talking more about the viewer view point, not really the characters...now there where so many similar mangas in which the seme was the one doing the same thing the uke did here, and was dragged down by the commenters (for right reasons of course), here there is almost no one mentioning what happened. As a viewer living in a different society with different ideals then the ones in the manga, it should give us a different look at things that were normal then...thats what schooked me, not how the uke reacted.

Again I am never one to be too mindful about fictional stuff or get too pissed about these stuff, but the ones that do get pissed at times are right.

I completely agree with you...many times the authors who write yaoi stories are females and even if that's not the case, it will be delusional saying that yaoi isn't meant to be a kind of porn addressed to girls. The uke most of the time (not always) is exactly a girl in men clothes, so we tend to relate to him more than the seme...thats how things are, I guess. That's why we tend to justify him more, becuase in most cases we see ourselves through him. Thats completely understandable, but at the same time also a bit sad...