To start with, the numbers are simply against this. By some estimates, as many as 1 million books are published in the US alone each year (here's some outdated numbers). Most of those are not fantasy, and no more than 1/500 (worldwide) or 1/50 (US) would be expected to have Jewish protagonists based on chance, but even if fantasy constituted 1% of all books published, and only 1/100 as many Jews appeared in fantasy as would be expected (extreme assumptions), we'd still expect around one fantasy book with a Jewish protagonist in the US each year.
More concretely, the list of fantasy with Jewish protagonists is very long. People will disagree on what constitutes fantasy, both because of blurry genre boundaries and because it's hard to discern whether authors believed in the earliest stories (the Golem of Prague?). I'll just provide a few examples:
The play "The Dybbuk," is extremely famous, dates back to 1913 and has a Jewish protagonist and a heavily Jewish background. It features clear fantasy, such as "demonic possession," summoning spirits, and miracle-working, much of which is inspired by Jewish folklore.
Isaac Bashevis Singer wrote many fantastical short stories with Jewish protagonists, including at least "The Jew from Babylon" as early as 1971.
As mentioned in a comment, The Golem and the Jinni has a Jewish protagonist, and is a contemporary work of fantasy. It was published in 2013, several years before Spinning Silver.
There's a notable tradition of Jewish reworkings of anti-Jewish works, such as "The Jew in the Thorns." One example of this is “Among the Thorns,” whose protagonist is the daughter of said Jew.
There may well be earlier examples, but this should be sufficient to establish that Spinning Silver, published in 2018, was not the first example of a Jewish protagonist in fantasy. There's a long tradition of Jewish fantasy.
One should also keep in mind that explicit Christianity in fantasy, or fiction generally, even among main characters, is not as common as one might think. It thus becomes difficult to say whether a character is definitively Christian or not. Or, to use more specific example, are the protagonists of The Reckoners series by Brandon Sanderson or The Beyonders by Brandon Mull practicing LDS? Maybe they are, maybe they aren't. Their religion isn't terribly relevant to the fantastical plots, so it isn't really brought up, as I recall. Similarly, explicitly Jewish characters are probably outnumbered by those whose religion is unstated. This is further complicated by the wide gap between a male Hareidi Jew, for instance, where any description of their appearance must make their religion obvious if not seeking to mislead the reader, and for example a secular Reform Jew who might not think about religion much except four or five times a year.
So assessing the frequency of Jewish protagonists by seeing how many are mentioned as explicitly Jewish can be misleading.