When I first played F/SN with Mirror Moon's complete translation patch, I too thought that either Shirou or Nasu was amazingly sexist, but I wrote it off as par for the course and soldiered on, as I was not really in it for the self-insert protagonist I had come to expect from anime-related entertainment.
Thus it was much to me surprise and delight when the story revealed that Shirou does not actually believe a word of what he was saying about women at all. When we learn about Shirou's traumatic childhood, we see why he awkwardly sputters out his lines about how he needs to stand between an insanely powerful magical conjured bodyguard and the lethal danger approaching her, and it has nothing to do with him being so dumb that he actually thinks he's better suited to absorb damage than her on account of having a penis. His motive is irrational, but it is not sexism - it's survivor's guilt. Throughout the events of all three routes of Fate/Stay Night, Shirou repeatedly goes out of his way to take the brunt of any danger approaching anyone who aren't his enemies, and sometimes even those who are. Only in the case of women does he use the excuse that men should simply protect women, and even then, his manner of speaking makes it clear that even he isn't really buying it. It's a deflection he's using to lie not only to the recipient of his ridiculous protective urges, but also directly to himself about his true motivations.
Of course it's off-putting the way Shirou immediately jumps to justifying his insane actions as male-to-female paternalism. It's supposed to be off-putting and weird. It's the first big clue the audience receives that something isn't quite adding up in Shirou's psyche. His white knighting is rooted in personal trauma, which has nothing whatsoever to do with sexism. Shirou's survivor's guilt complex is the pivotal theme of the entire story, and in Heaven's Feel, he is finally brought around to discarding this complex so that he can live his life unburdened of the psychological disorder which has seared his mind since early childhood.
Removing this blatant "sexism" from Shirou's words cheapens the significance of their hollowness and damages the depth of the story itself, which centers around Shirou's development as a character.
Post too long. Click here to view the full text.