This is the side of shoujo that I never really liked. Yeah, there’s the “twist” that he likes being protected, but the overall undertone is that she should just be “womanly” and be protected. Even if eventually the story validates her choices, the undertone stays.
And I’d argue that men protecting women is not a natural instinct. Women are put in overall vulnerable positions by men, and then told they should allow the men to protect them. The women are never allowed to protect themselves, or escape the vulnerable positions they are in, which always struck me as weird.