There was nothing in a goalless first half but United fell apart after the restart when a defensive mix-up allowed Kieron Bowie to break the deadlock.
Sam Hoskins added a swift second, his tenth of the season, and that proved too much for Cambridge to come back from despite Gassan Ahadme scoring late on.
Cambridge have just one win of their last 12 League One games and are now 16th in the table.
“The first half was fine and we chased it well enough at the end but we gave the game away with two hopeless goals in a five-minute spell at the start of the second half,” said Bonner.
“We were OK and had a couple of half decent chances, both teams did, and defensively we were doing OK, but it doesn’t matter as we’ve giftwrapped a game that we should never have lost.
“The goal just after half time is a hopeless goal to give away. We looked vulnerable and they caused us problems when they played forward.
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