As far as I know there is no scientific reason why one couldn't light a candle in a spaceship because, as you and Wakerra commented above, a manned spaceship is designed to have a similar atmosphere to that on earth to support the humans onboard. I think, however, that the close quarters of a spaceship--meaning you are within close proximity to many things like oxygen tanks that can explode--is the main reason why you can't light a candle in a spaceship. A close secondary reason is as Wakerra said: the amount of oxygen on a spaceship is limited, and candles would use that supply up quickly and needlessly as well as mess up the air filtration systems.
Yet another reason is that, without gravity and with the constant atmosphere on a spaceship, I think it would be hard/impossible to extinguish a candle, let alone safely. You would either have to pinch it off with your fingers or cut off the wick and wait until that wick has burned itself out.
If fire is to be used inside a spacecraft, such as to perform a scientific experiment, I imagine it would need to be done within a closed box, much like an incubator.
Also, because the Apollo 1 mission burned up and killed all of the crew on the launchpad in early 1967, I think NASA is particularly sensitive to this subject. Conditions inside the cockpit are totally different now, mimicking the earth's atmosphere and not pure oxygen as they were in Apollo 1, yet that specter haunts us and the space program today: three heroic astronauts died that day. The American people have essentially a zero-tolerance for death and failures in the space program; an unrealistic expectation, in my opinion, that is holding us back greatly.
Note that welding and soldering torches can be used outside the spacecraft because the source of gas is provided and can be turned off with a valve to extinguish the flame. That is how the space shuttles were repaired in space and how the international space station is being built: with real welds, not SuperGlue. ;-)