Update from Salesforce support:
I checked with R&D regarding this, and they are releasing an enhancement to allow all modifiers in the next version of the API, which is 34 (Summer '15). -Shashank
It appears that at the API level
protected isn't supported.
Extract from the Tooling API v32.0 WSDL:
Note the absence of
protected. It can't be returned, so it appears they send back
You also see hints of this in the documentation for SymbolTable:
It does seem odd the protected isn't represented, as it is valid in Apex access modifier.