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I think Sakura beating up Naruto is a little different then other tsundere relationships since some people see Naruto as a "door mat" who full on takes Sakura's beating without any sort of retaliation. I admit I did have a problem with this myself at first but after the Gaara fight at the end of the Chunnin exams that washed away my issue with it and didn't bother me since I saw Naruto's devotion to Sakura. However, the majority of the fandom would see otherwise since it seems as if Naruto takes on the abuse of Sakura and doesn't say/do anything about it (and the anime plays this up a lot so it seems really overblown).
* Nami/Luffy isn't really a tsundere relationship since Luffy is pretty much assexual and well...he's an idiot (but still a cool idiot of course).
* Rukia/Ichigo works both ways since Ichigo isn't afraid to insult Rukia (he calls her a b*tch quite often) and smacks her just as much as she does him.
* Asuka/Shinji....well Shinji well on deserves all the abuse seeing how his personality is. And he has choked the hell out of Asuka and even left her to die in EoE so it seems a fair bargain.
I'd say NaruSaku is pretty comparable to KeiNaru from Love Hina and RanmaAkane from Ranma ½. Both male leads tend to take on the brute force of their love interests without "striking" back at them. And just like Sakura, Naru and Akane are tended to be really hated within their respective fandoms for this reason. Not all tsunderes are created equal; it depends on how the author of the series defines the relationship between them and their male counterparts.
I can't talk about Love Hina, but Ranma/Akane isn't comparable in the sense you mean. Ranma yelled back and insulted back, and often picked on Akane for no reason. And, personally, I never hated Akane. As far as I have seen, her haters usually hate her because she's in the way of their favoured pairings. She being violent is nothing but an excuse because they ship Ranma with girls are more violent Akane, or have struck Ranma a lot of times or have abused him, exploited and disrespected in every way, shape or form.
Now, even if I agree with your last sentence, I yet can't see the difference. And frankly, I don't understand why it's a big deal or why some people make an issue of it.
Sakura's blows -which are very overplayed in the anime and whose importance, frequency and lethability is way overblown by the anti-NS fandom- never bothered me. The first time I saw Sakura yelling at and hitting Naruto right after he thought he liked her, I thought: "I wager they'll end up together". The thought I ought to take seriously her outbursts of violence never occurred to me.
On topic. It's true you find less NaruSaku fics using the character filter, but it doesn't bother me. Our shipped pairing isn't so popular like others, and the character filter is a relatively new feature. Thus, there're many old NS stories it doesn't find. And I also preffer quality about quantity. I don't require more NS fics than non-NS ones in FF.Net. I require they are good.