Jim, let me go over a few things for you:
1.) Statistics for rape by gender are incredibly unreliable. For starters, the legal codes in most countries define rape as a crime only a man is capable of committing. In the UK, for instance, female rapists cannot be charged as such because the act of rape requires having a penis. The most commonly quoted rape statistics for the US come from the NCVS, a survey which defined rape purely as a penetrative act. This meant that the only female rapists counted were the ones that used strap-ons and that most victims of female rapists, female as well as male, were completely erased. The successor to that survey, the NISVS, counted rape by envelopment but listed it under "other sexual violence" as "forced to penetrate". This meant that the majority of male rape victims were not counted in the "rape" statistics and female victims of female rapists were still completely erased. Rectifying this error in categorization gives numbers far closer to parity for both perpetration and victimization. However, these numbers are still not terribly reliable because the NISVS has come under heavy criticism for using definitions designed to inflate their statistics far beyond the actual instance of rape in the US. This leaves out rape in prisons, where some estimates place the number of male victims in excess of those in the civilian female population and recent studies have shown female guards to commit a disproportionate number of rapes (often framed as "relationships" or the woman being "seduced" when reported in the media). In the Congo, rape of male captives is a widespread cultural practice ignored by both international media and aid organizations.
2.) It is a blatant falsehood that society does not tell men not to rape. Upon entering university, I was required to attend three separate programs on how not to commit rape (current legal definitions mean that it is often possible to do so entirely by accident). Female students were exempt from all three sessions and no mention that men could be raped or should take precautions against being rape was ever made. Indeed, I did not hear about men being raped outside of prison until it happened to someone I knew. As you yourself mentioned, rape is seen as a horrific crime in our society. Where are these messages telling men that rape is okay?
3.) It is incredibly dishonest to frame rape as purely or primarily an act of physical force used to overpower a victim. The majority of rapes in our society involve the use of drugs or alcohol to render the victim incapable of resisting, or the use of social or economic pressures to force their submission. Men are just as susceptible to these methods as women, and it is incredibly dismissive and dishonest to say they have nothing to worry about. That the average man does not fear being raped is not a testament to his protection from that possibility, but to the fact that no one has ever educated him of the possibility or warned him to be careful.
You are, however, generally correct in your reasoning as to why rape is both less common and less okay than murder in games, although I think you significantly underestimate the effect depictions of graphic violence can have on victims of actual violence (they don't all die, and it can be every bit as traumatic).
