Rust is cancer. It will not stop growing once it gets established. It will cause the tank to flake off and will eventually clog your fuel filter, fuel injectors or your carb. The only fix is to pull the tank, have the inside descaled and then recoated to prevent further damage.
+1 on what Skrapiron said. I had to deal with rust in the tank first hand. Best thing you can do is get the rust removed and tank relined. It is still a temporary solution (several years, depending on your riding & conditions), as the coating will eventually start to flake-off, and will need to be reapplied. It is not all bad, but be on a lookout for it.
If coating the tank yourself, there are about a 100+ ways of removing rust and getting the tank coated: happy googling. Just make sure to remove the fuel pump assembly before adding rust remover and coating agents.