One: an infant is easier for the clans to control. Since the death of James V at Flodden, Scotland had been ruled by committee.
Two: She married without her counsel's advice/or against it (like any one of them would vote for a Englishman whose only recommendations were his looks and charm with ladies).
Three: She was Roman Catholic, and despite her neutral position on religion, the Protestants were taking no chances on losing their religious control.
Four: She didn't kill Darnley, she didn't have him crowned & for that latter reasons, a few good Scotsmen decided he was (to quote an Elton John song) 'better off dead'. But when Bothwell was acquitted, she didn't do the smart thing - banish his ass back to his estates (there were more than enough nobles from both sides of Scottish blankets to enforce this.
Five: She was too easily swayed by a pretty face and manners OR a man with a great ego and the strength to back him up.
Six: Since they (the nobles) wanted #1, they used Bothwell's apparent ravishment of the Queen (which should have been TREASON to get rid of her.
Seven: Last but not least, it's the same attitude H8 had regarding having no son - Women can't rule, can't hold a throne (apparently his first mother-in-law had be totally forgotten by Hank).