Dean Thomas’s father was a wizard killed by Death Eaters. He never told Dean’s Muggle mother that he was a wizard because he did not want to jeopardize his family’s safety. His concerns were not unjustified because he was recruited by Death Eaters and murdered by them when he refused to join them. Dean was very young when his father died, and he grew up believing his father to have been a Muggle who abandoned his family (JKR).
Other canon notes and references
Dean's mother later married Dean's stepfather, Mr. Thomas (OP11, JKR).
From the Web
Pottermore feature: Dean Thomas's Hidden Storyline