There are two possible reasons: one involves cultural custom, the other involves the influence of money in politics.
Tobacco has been a cash crop since the Colonial era. James I reaped a great deal of wealth from Virginia's tobacco trade. After independence, Virginia emerged as wealthiest Southern state. Though tobacco fell out of favor for a while as a major cash crop, in favor of sugar, rice, and cotton, it has never disappeared from industry. North Carolina also became known for its tobacco trade.
Regular cigarette smoking has, until recently, long been perceived as normal and permissible, along with drinking alcohol. Anyone who watches old movies will eventually see someone light a cigarette. Marijuana, on the other hand, has always been associated with people who are outside of the mainstream: jazz musicians (hence, an association with black people and black culture), the Beat Generation, and hippies.
Views around marijuana did not begin to change until the 1990s, when more research was conducted to discover the drug's medicinal uses. However, the idea of legalization was still regarded as radical in many states. In the same decade, the tobacco industry was forced to take responsibility for its past unwillingness to warn people about the dangers of cigarette smoking. They paid millions in lawsuits to the families of those who died from cancer and emphysema. They also began their "Truth" campaign -- a series of commercials directed at teenagers to discourage smoking among youth.
However, the tobacco industry is also a very powerful political lobby, meaning that they can influence politics and policy with their wealth. The tobacco industry is not unique in this regard. All powerful industries, including food and fossil fuel industries, use their wealth to support the political campaigns of politicians. In turn, they often receive cooperation, in the form of legislators voting against laws that could hurt the respective industry. The tobacco industry might have an interest in suppressing the support of legislation that legalizes marijuana.
Finally, efforts to legalize marijuana have mainly been carried out at the state level. Washington State and Colorado have legalized marijuana. Other states, such as Colorado's neighbor, Nebraska, are hostile to the industry. Nebraska is a much more conservative state. Conservative states, particularly those with large elderly populations, tend to be less accepting of marijuana. As I previously mentioned, marijuana was associated with counterculture. Also, certain anti-drug films, such as "Reefer Madness," fueled paranoia around marijuana use with the suggestion that marijuana could cause people to leap from windows!