There are many points that must be brought up in answering this very interesting question.
First, we must realize that economics does not claim that people choose their goals rationally, only that they choose the means to achieve those goals rationally. For example, economics does not say that people will rationally choose what kinds of food they like, just that they will think rationally about things like how much to pay for the foods they have chosen. Thus, there is not necessarily any contradiction between the idea of rational choice and smoking.
Second, economics does not claim that all individuals will act rationally in all instances. Economics does not generally claim to be able to predict the behavior of any given individual. Instead, economics claims to be able to predict the average behavior of large numbers of people.
Third, we have to realize that some people become addicted to cigarettes and can therefore no longer be rational on that issue. They have come to have a physical need for the cigarettes.
Finally, let us think about why a person who is rational might choose to smoke cigarettes. The important thing to remember is that cigarettes provide some degree of benefit in the short term while the negatives of smoking are less certain and are not immediate. If you enjoy smoking, you know you will gain that benefit and you will do so as soon as you smoke the cigarette. You do not know for certain that your health will be harmed in important ways. You might be one of those people who lives to a ripe old age even as a smoker. In addition, the harm that may happen to you is not likely to happen for a long time. Given these things, it can seem rational to accept guaranteed benefits in the short term at the risk of possible costs in the long term.