dev-libs/protobuf is needed as an optional dependency for net-misc/quagga-1.1.0 and above. I have masked it currently in hppa profile(despite message in header of the file, sorry for that). I see that old protobuf marked -hppa, so, if it is not possible to run protobuf on HPPA hardware, please close this bug as WONTFIX, thanks in advance.
did you mean to ask for a STABLEREQ ? as Jeroen points out, ~hppa was added long ago and is still in all newer versions.
No, i was just blind enough to see that dev-libs/protobuf-2.6.1-r1 is already have ~hppa ;-)