If you were going to make your own tubes from transparency sheets, you could cut a circle of cardstock about twice as big as the opening on the end of your tube, trace the tube in the center of the circle, cut in from the edge to the line you've traced all around the circle (so you make a kind of flowery looking circle), and fold those tabs up. Then you'd have a sort of cap you could slide into the end of the tube and a surface to adhere the punch outs on the ends. You'd have to use some sort of adhesive on the bottom "cap", because the weight of the M&M's would almost certainly push it out.
Definately easier and quicker to find tubes that have little plastic caps for the ends!
Really cute idea! Would have made a cute end of the year treat for the kids (but today is the last day of school for my DD) -- something like "seeds for summer fun" -- blue for pool water, yellow for sun, red for sunburns . . .