The hosts were ahead within four minutes when Josh Coulson sent Harrison Dunk's cross towards Williamson, who fired home from close range.
Yeovil had Liam Walsh dismissed after 10 minutes following an off-the-ball altercation with James Dunne.
Dunk teed up Williamson to score again before the break, before James Spencer wrapped up three points late on.
Cambridge United ended 10-man Yeovil Town's four-game winning run in League Two thanks to Ben Williamson's brace.