I don't think Tohru's attitudes are very typical of Japanese culture. In fact, the other characters in the Furuba universe (while all pretty outside the mold themselves) are often shocked by them. I read it in Japanese so I'm pretty far ahead of where I'm guessing you are and I don't remember the beginning very clearly, but I feel like it came up a couple of times how excessively polite her language is, and I think everything about her is like this. It's almost like she's an old-school ideal of Japanese femininity taken out so far to the nth degree that she out-cultures her own culture and winds up confusing them. For a while I had trouble getting into Furuba (which is now one of my favorite manga) for this reason, but eventually I realized that (as I think gaudior has said), for every creepy extension of Perfect Nonexistent Japanese Womanhood that Tohru exhibits, she also has a subversive and under-the-radar atypical trait (like her devotion to protecting her lifestyle with three young men, the fact that she hangs out with gangsters, her tendency to involve herself in other people's problems, etc.). And she does have her own issues, and some of her responses spring from more complex places inside her than the typical manga heroine. So yeah, those things made me like her and the manga itself a lot more. But the sort of base set of patterns and behaviors that is Tohru seems much more to me like a commentary on Japanese culture than like a typical representation of Japanese culture.

(Sorry, we don't know each other--I'm a Japanese-English translator, so these are issues I think about rather a lot.)