In 2005, my paper on breaking RSA by observing a single private-key operation from a different hyperthread sharing the same L1 cache -- literally the first publication of a cryptographic attack exploiting shared caches -- was rejected from the cryptology preprint archive on the grounds that "it was about CPU architecture, not cryptography". Rejection from journals is like rejection from VCs -- it happens all the time and often not for any good reason.

(That paper has now been cited 971 times according to Google Scholar, despite never appearing in a journal.)