I've used two methods. The thickness of the tube determines how I do it.
For thinner tubes, I just use an xacto knife and go very slow. Don't try to cut the tube all at once. Use many lighter strokes. Just keep going over it until you are through. This way, there's more control than if you were to try and jam it through all the way.
For thicker stocks, I've used my dremel tool with a fibre cutting disc. Very slow, very carefully. I also tend to do one very light cut to determine where I want it to be and then do a heavier all the way through cut.