Bonner attended A.C. Jones High School where he earned a total of nine letters (four in football, four in track and one in basketball). He played quarterback in football, recording 3,180 passing yards and 2,477 rushing yards in his career. As a senior, he was named All-South Texas Quarterback and Offensive Player of the Year by the Victoria Advocate. He was offered football scholarships at Georgia Tech, Houston and SMU but elected to play at TCU.
College career
During Bonner's first two years at TCU, he saw little action. He redshirted in 2003 to make the transition from quarterback to safety, and was used sparingly in 2004. In 2005, Bonner led the team with four interceptions, two of which came in a win against Colorado State, which clinched the 2005 Mountain West Conference championship. As a junior in 2006, he was named first-team all-conference as a punt returner and second-team all-conference as a safety.