Are you using a multi-tap? Try it without.
I haven't played this game in a while but if I recall correctly it's something like: Hold button to shoot regular shot and release it to shoot the beam. Or maybe it was tap button for regular, hold for beam... something not terribly complicated anyway.
There's an invisible beam meter of sorts, I believe, which 'fills' as you hit stuff with your regular shot. But it fills very quickly and it's rare to not be able to use the beam.
If you still can't figure it out, I guess I'll dig out my copy later and give it a play. (Probably will anyway--it's a very fun game)