Okay, my motto is to always use a lens hood. A lens hood reduces any stray light that you don't want in your image in the first place. This is important, especially with the lights on a stage. A lens hood will not darken your picture in any way, it just prevents flares from other lights. (+ it's a great impact shield for your lens)
The only time you need to take off your lens cap is when you use your popup flash, or it will cause a nasty shadow on the bottom. This may even happen with the shortest focal lengths if you have a long lens, so experiment with that.
Secondly, bump your ISO. Stages are often poorly lit, and I had to set my ISO to 1600 to get sharp pictures. This also helps freeze people in mid-air if they do their moves.
Third, set your camera to centre-weighted or spot metering. I found that the normal metering grossly over-exposed the frontman, and underexposed the others behind him. The soundcheck is a great moment to check your lighting.
About flash: I talked it through with the band, and they weren't very fond of flashes. Combine that with the supreme noise performance of my camera and image stabilisation, and there's no trouble at all.
You don't want to be that annoying person blinding everyone, that certainly does not make you popular amongst the band and crowd.
If they are okay with it though, flash moderately
Thanks for the kind comments, and if you have any more questions feel free.
EDIT: here's a page about lens flares, and the use of lens hoods. They have pictures and explained it better than I can.
http://www.cambridgeincolour.com/tutori ... -flare.htm