Except the Autobots don't really act like an army, nor do they really have the numbers to call themselves that. They're a single small unit, and while the threat from the enemy has steadily grown, it's still diminished from what it was on Cybertron. In that situation the interpersonal relationships are important. While Optimus wasn't able to control Wheeljack as well as he does, say, Bumblebee, he was at least able to manage him and work with him when necessary. Magnus can't even do that. He only sees the broken rules and not the rulebreaker. It's an immediate problem for Wheeljack but it will be a problem for the other Autobots as well, and eventually for Prime. In a small, tight-knit group like the Autobots on Earth, being a stickler for protocol like Magnus isn't helpful. He needs to focus less on how the job is done and more on getting it done. Even Ratchet, the most stubborn and set in his ways of the Autobots prior to Ultra Magnus' arrival, understands this and is able to be flexible. Ultra Magnus insistence on a rigid chain of command and by the book approach will eventually be as much of a problem for the Autobots as Wheeljack's insubordination. I'm not just saying this because I like Wheeljack (Ultra Magnus across all his incarnations is one of my favourite characters in the franchise) but because that's how it is. The Autobots aren't a huge army with multitudes of troops. They're a small unit more comparable to a football team or a small company, and in that situation, people are more important than protocol.