As Vice President, Lyndon Baines Johnson ascended to the Presidency upon JFK's death. As such he was one of the people who benefited most directly from the shooting. Since most conspiracy theories involve some sort of government collusion in Kennedy's assassination, they require a high-placed government official to be behind them, and LBJ would fit the bill. Also, most conspiracy theories posit the desire of the "military industrial complex" to escalate the Vietnam War as being the motive behind the assassination. LBJ ended up radically escalating the US involvement in Vietnam into a full blown war. For members of the anti-war movement at the time, Johnson became something of a villain, as expressed in the chant "Hey Hey LBJ, how man kids did you kill today!"
The public personae of JFK and LBJ also marked them as different men in the public imagination of the time. JFK was a young, handsome, and charming playboy. A political moderate, JFK flirted with issues like Civil Rights but took little radical action during his times. After his death a lot of people remembered his administration fondly and many people were able to attribute whatever ideas they wanted to JFK. For many people, including conspiracy theorists, this included the idea that JFK would have gotten us out of Vietnam. At the time of his death Vietnam was just one front in the US war against communism and not that important to the American public. A few years later, Vietnam had become the biggest foreign policy issue for the country and had provoked massive public protests. In this atmosphere, it was comforting for many to think that Kennedy, the martyred President, would have removed US forces. In contrast, LBJ was a much more prickly personality. He was famous in the Senate for browbeating people into submission. As an old school Southern politician, Johnson was often more comfortable with the nuts and bolts of politics than with the high flying symbolism of the Kennedy era. At the same time, Johnson had a much more radical agenda than Kennedy did. His Great Society and Civil Rights programs sought major changes in American society and provoked significant discord from those who disapproved of them. In addition, Johnson escalated the war in Vietnam, a decision which ultimately doomed his administration when the war became unpopular with the country at large.