The scene looks like this: they go to seme's place, and the uke says, "You're wrong, I don't intend to..."
They enter, seme slams the door, pushes uke and grabs his ass, saying, "This is fine, right?" Uke is trying to answer: "N..." [...] "Se... sen... se- that's not..."
Seme proceeds with sex. Uke has a realization: "Ever since I heard that story... what kind of face does sensei make... how does he have sex... If I were a female student... I've fantasized about the worst things over and over. I'm sure if I knew the reality... I'd realize he was an awful teacher. My memories would be destroyed. And I'd hate him... supposedly."
Later or [different scene] seme admits that there was force and no consent.
There are different legal definitions of rape. In the past, in many countries, the word applied only to situations when physical force was used, and the raped person physically fought back, and it didn’t apply to married couples at all. Fortunately, nowadays there is more awareness about:
a) situations where people use not physical force but manipulation, power imbalance, pressure, situations where another person is not able to give consent etc.,
b) various factors like psychological shock, fear, being manipulated, being under the influence of substances, etc., which may prevent people from saying "no" or physically resisting, even when they don’t want sex,
c) harmful consequences of sexual abuse is, especially psychological demage.
So, taking all above in consideration, new definitions of rape are based on consent. Here, there is a situation where:
a) seme didn’t ask for consent and used force,
b) uke didn’t give consent; on the contrary, it looks like he was trying to say "no"; additionally, it was just after being in a bar — if he was drunk, he was not in a condition to give consent, and alcohol could make it harder for him to say "no" or resist,
c) uke’s realization implies that now he experienced rape and knows that it’s awful, not as it was in his fantasies - he suffers because of what happened.
So this was rape. Rape cannot be explained as a "misunderstanding."
Imagine a situation: one person grabs a wallet belonging to someone else, saying, "This is fine, right?" and after hearing "n...", just takes it. Would you say, "It was not theft, just a misunderstanding; they just assumed that the other person wanted to give them the wallet"? Unwanted sex is much m ore harmful than loosing a wallet, how could it be excused by "misunderstanding" of a person, who didn't ask for permission? Sex requires explicit consent given freely, without pressure in a situation when a person is able to consent [age of consent, being fully conscious and aware of the situation and possible consequences].
"...he was rough and it hurt the uke but i thought this was all more emotional hurt rather than a crime of violence" - There are various types of violence: physical - causing bodily harm, sexual - any non-consensual sexual act, psychological - undermining self-worth, causing emotional pain, financial - eg. controlling access to money, preventing a partner from working, coercive control - using different methods to dominate another person, neglect... Lack of physical pain doesn't mean lack of violence.
In this manga, there was sexual abuse, a type of violence that has elements of both physical abuse (it violates physical integrity and often causes physical pain) and emotional abuse (one person dominates another and causes emotional pain, often having a negative impact on self-image and self-esteem). A rape victim who didn’t fight back often blames and detests themself, and has less evidence against the culprit — it doesn’t make the act any less of a rape.

Maybe I got the wrong impression but until I checked the comments I didn’t think there had been any rape. ??? Yes i thought they misunderstood each other and he was rough and it hurt the uke but i thought this was all more emotional hurt rather than a crime of violence. And they talked and got to know each other better so whats the problem? They got over their traumas together and that was it they are happy