Huh, that reference actually never occurred to me.
The name Cap'n Proto actually originally meant "Capabilities and Protobufs" -- it was a capability-based RPC protocol based on Protocol Buffers. However, early on I decided I wanted to try a whole different serialization format instead. "Proto" still makes sense, since it is a protocol, so I kept the name.
The pun "cerealization protocol" is actually something someone else had to point out to me, but I promptly added it to the logo. :)
https://memory-alpha.fandom.com/wiki/Captain_Proton