I should say I think singling out, without qualification, is not enough for anti-Semitism. What is required is a prejudiced or irrational singling out, like holding Jews, even those born today, as especially perverse for rejecting Christ.
But there are ways, perhaps, you might single out Judaism without being anti-Semitic. If, for example, you were a sceptic who felt religions with particularly extensive religious laws were especially silly and pernicious, then you might single out Judaism and Islam (and perhaps a few other faiths) as even worse than other faiths. I don't think this would amount to anti-Semitism because it is based on a rationally defensible point about the nature of religions, and not any irrational prejudice against Jews. But if you disliked Judaism for this quality but not Islam, then this would suggest some kind of prejudice.