I don't see atheism and skepticism as a gateway to alt-right ideology, any more than marijuana is really a gateway to heroin. But that doesn't mean that the alt-righters won't still sully the movement if we welcome them to participate in it.
Sure, it's true that some alt-right YouTube personalities self-identify as "atheist" and/or "skeptic" as a marketing angle. But I see it as no different than the NSDAP appropriating the word "sozialistische" to leverage the popularity of socialism to attract politically unsophisticated working class people. Dorks like

are really no more skeptical than any other hardcore ideologues. They exhibit excessive dogmatism, confirmation bias, denialism, FUD, and loaded language, and much of the false information they tout is actually rooted in some of the world's oldest conspiracy theories. They're just piggy-backing on the existing skeptical movement and convincing their followers that their bigoted views are part and parcel.
I believe this kind of outcome is why early skeptical leaders (like CSICOP founders Paul Kurtz and Carl Sagan) argued that the movement should only be promoted within the realm of academia.