HP,
I could argue that in 2 ways a government has the right to make a substance illegal.
1) when the consent of the governed asks for it. This is why anything should be legal or illegal I would say. If we believe in a democracy, or a republic as we have, that the right to govern comes from the consent of those governed, then when the people consent to have certain things made illegal; they are.
2) In the history of western philosophy, particularly political philosophy, a person does not belong only to themselves, but also to the larger community. This is always something held in balance. It is why conscription to armies can be legal, why suicide in most western countries historically has been illegal. Because your life is not entirely your own. There are consequences and costs associated with certain actions, and the government has a vested interest in your behaviour.
That is a VERY VERY fine line to walk I understand. Drugs are illegal, but sodas aren't? That type discernment is VERY difficult to make. I rely primarily on point 1 when it comes to such disputes. What is the consent of the governed?