Someone with Uncouth isn't just ill-mannered, they "have trouble interacting with others." Maybe they don't even understand what would be intimidating to someone, maybe they stumble over their words so they look like a baby having a tantrum instead of being scary, maybe they don't pick up on social cues and try to intimidate the weasel of a gang instead of the gang leader, maybe all kinds of stuff.
They can still stand there and be a menacing presence for someone else to make an Intimidation test (the fast-talker who always knows what to say and how to say it just thumbs over his shoulder to a hulking brute looming behind him), they can still offset the Uncouth penalty (and no doubt a low Charisma, and no doubt a not-too-great skill) with modifiers for being big and scary...but...well...if you want to be good at making people do what you want (which is what Intimidation checks are for), don't take the Negative Quality that boils down to "you're terrible at making people do what you want."