It isn't just that the other characters aren't dominant. They actually don't seem to mind Daria that much. They can't really relate to her, but they don't reject her outright either. Daria's isolation at school seems to have more to do with her rejecting her peers, rather than vice-versa. Some of that may be "reject them before they reject me" as Eric mentioned (and this came out a couple times during the show). She also has high moral standards that can cause her to clash with others (which is pointed out several times by other characters on the show) and prides herself on her ability to see things others can't (Fi and Ni?). A number of her schoolmates seemed to have respect for her, even if they didn't consider her part of their social groups. She may be isolated and jaded, but it isn't really because the world has shut her out. It's more something she imposed on herself.
Obviously the characters aren't real, and Daria doesn't really exist and so does not really have cognitive functions and all. I don't see how that changes anything. You can still look at what she says and does and how she reacts, and decide which type her words, actions and reactions best fit. Why does it matter exactly how the character was cobbled together? We can never really know that anyway.
And who's saying she's an ISTJ because she doesn't get beaten up? People are talking about cognitive functions and interaction styles. What is the argument for her being INTP? I haven't seen much; people just seem to be assuming that a nerdy, sarcastic, passive loner must be an INTP. Often, but not always.
Personally, while I liked the show as a teenager and felt similar to her in a number of ways,
I sometimes did not understand why she'd get so bothered over certain ethical matters. For example: feeling ashamed of caring about her looks enough to try contact lenses, getting angry at Jodie when she mentioned her father's name in order to get a banker to approve her for a loan, complaining about soda advertisements in her school (she thought it was sleazy and took her complaint right to the company, IIRC). Stuff like this doesn't strike me as very INTP-ish.