The shell ignores the "opQueryOnly" and "opCommandOnly" values for the --rpcProtocols option. When either of these options are passed, the shell treats them the same as the default option "all".

Reproduce with the following script:

db.runCommand("ping");
var logs = db.adminCommand({getLog: "global"}).log;
print(logs[logs.length - 1]);

See the following shell session, which was run against a 3.2.0-rc4 mongod started with the -v option. Even though the "opQueryOnly" option was specified, the diagnostic log line for the command shows protocol:opCommand, which is unexpected.

rassi@rassi:~/work/mongo$ mongo320rc4 --rpcProtocols opQueryOnly repro.js
MongoDB shell version: 3.2.0-rc4
connecting to: test
2015-11-25T14:04:40.908-0500 I COMMAND  [conn2] command test.$cmd command: ping { ping: 1.0 } ntoreturn:1 ntoskip:0 keyUpdates:0 writeConflicts:0 numYields:0 reslen:22 locks:{} protocol:op_command 0ms

See the following shell session, which was run against a 3.0.7 mongod started with the -v option. Even though the "opCommandOnly" option was specified, the diagnostic log line for the command shows the server as correctly having received the command request, which is unexpected.

rassi@rassi:~/work/mongo$ mongo320rc4 --rpcProtocols opCommandOnly repro.js
MongoDB shell version: 3.2.0-rc4
connecting to: test
2015-11-25T14:04:08.317-0500 I COMMAND  [conn2] command test.$cmd command: ping { ping: 1.0 } ntoreturn:1 keyUpdates:0 writeConflicts:0 numYields:0 reslen:37 locks:{} 0ms

This is a regression introduced in 3.1.7 by 2a6a8f7c (SERVER-19376).