In the manja, is a male being harassed by a female presented as something that it's normal for him to dislike? As funny? As sometimes a serious problem for him?

Yes, all of these. Will depend a lot on the author and what kind of crowd they want to reach (or just what they enjoy producing). I'm guessing at least half portray it as actually negative and something that should be prevented. A significant fraction of the other half probably don't for "people are supposed to masturbate to this!"-style reasons.

It being "normal for him to dislike" is slightly less common as far as I'm aware, but the large prevalence of oblivious male characters who don't respond well and don't have particularly strong desire for sexual interactions with females explicitly and overtly trying and wanting to have some with them (in non-erotic anime and manga especially) should serve at least as some evidence that it's at least not a completely alien concept.