Being Speaker of the House of Commons is a tough job at the best of times. Not least with MP's trying to flex their muscles and some thinking they can get away with bad behaviour. It's not often though that the miscreants include the Chief Whip.
Tory MP's tend to give John Bercow a hard time, not least because they think the Speaker should be one of them. It looks like it doesn't count that he works hard, tries to be fair, and is courteous. Some accuse him of being standoffish. Betty Boothroyd could be on occasion, and sometimes they accuse him of bias. Betty Boothroyd faced that as well, in fact if you read her autobiography it is clear that she didn't get along at all well with Richard Ryder, who was Chief Whip in the Major government, and he tried more than once to bully her, only to have it rebound on him!
Patrick McLoughlin can protest all he likes, but he heckled the Speaker and did so from the wrong position in the House and as Chief Whip he should know that is out of order and therefore should have taken the objection like a man. He didn't. If he had used the conventional channels he may have inspired some respect, even if he was wrong, but again, he didn't, and so the Conservatives have no right to complain.