Baron Harkonnen hated the House of Atreides because the Atreides started getting respect from the people. Though the Harkonnens were rich and powerful, they got hated because they were brutal and unforgiving. The Atreides, on the other hand, treated people with dignity; this made the Baron and emperor see them as a threat to their sovereignty and riches. Because the emperor and the Baron had a common hatred for the House of Atreides, the emperor borrowed Baron Harkonnen the Sardaukar to invade the Atreides and kill their governor, Leto.