There were a variety of factors involved in the decision to expel the Jews. Isabel and Ferdinand had many Jews in their Court; these were both Jews who had converted to Christianity and those who had not. Many of the leading lights of the Church - important bishops and even Cardinals - were converted Jews. However,there was considerable anti-Jewish sentiment among the people, probably stirred up by jealousy on the part of the barons and petty nobility, who did not like the prominence that Jews had achieved or their relative financial well-being (since Jews did not live by farming but by skilled artisanry or by finance or even, in some cases, by "knowledge work" - translators, physicians, etc.). There were riots and attacks on the calls (or semi-autonomous Jewish areas in Spanish cities). Finally, when Isabel decided that the Spanish Crown did not have the resources to protect the Jewish residents anymore, she ordered that they leave. Of course, she also ordered that they surrender most of their wealth to the state when they left, since the Spanish crown was aggressively seeking income to fund its project of unifying Spain, which was one of the sources of its conflicts with the barons, as well.
There was some feeling that the Jews were supporters of the Muslims, at least as far as lending them money for arms, etc., but this was simply another part of the anti-Jewish feeling that had been building among the jealous nobles and civil officials even prior to the victory over the Muslims. Incidentally, if you think Spain is bad, remember that most of Northern Europe didn't even have Jews; England, for example, had expelled its Jews centuries before, in 1290, after years of increasing restrictions and attacks.
In other words, it's a very complex history. The perception that the Jews supported the Muslims may have had something to do with some attacks on them, but a lot of it was much more complicated than that and had more to do with politics and the economic situation than with anything else. In any culture, Jews, who were at that time always perceived as foreigners but at the same time did not have the power of a foreign government behind them, were an easy target for any popular frustrations, fears and resentments.
There are other aspects of the history of the Inquisition that seldom get mentioned; that Torquemada was descended from Jewish converts to Christianity (his grandmother was Jewish, and that the Papal decree did NOT allow him to pursue Jews who practiced their Own faith, only the converts who "secretly" practiced Judaism. Which of course is a slippery slope to all out persecution.