The Federal government uses the Interstate Commerce Clause from the US Constitution to get at nearly every business, no matter how small. The entire 1964 Civil Rights Act was based on the Interstate Commerce Clause because without it, there was no way to prohibit discrimination by a private restaurants, bars, or stores. The Interstate Commerce Clause is a catch-all, because it basically says that the US Government can regulate anything that affects "interstate commerce". That has been stretched to include selling goods from out of state, selling to customers from out of state, or thinking about a relative who lives out of state.
In this case, the Supreme Court wasn't deciding the power of the federal government but of a state government. Because the constitution expressly states that all powers not given to the fed are reserved for the states, states usually have the power to make their own laws, provided that they afford at least the minimum protections afforded under federal law.
State laws have made smoking illegal under certain situations. Because there is no federal law protecting smokers or smoking (other than the millions paid to federal lawmakers by big tobacco), states basically have free reign to ban smoking so long as there is a reasonable basis for doing so.
Basically, Big Tobacco needs to spread their money around better, now filling up the coffers of state legislators and even city council members. C'mon Phillip Morris, stop complaining and pay up!