To make a flare ,or anything else with a black background transparent all you have to do is use the background eraser tool messing with the tolerance. You'l get a transparent flare pretty quickly.
Oh yeah, if you're making logos using flares, you're doing something terribly wrong.
I stumbled upon some great UI inspiration for all the designers. It's some real cool stuff and shows you what actual graphic design is.
If you haven't already make an inspiration folder in all your Photoshop stuff so you can hopefully become a better designer.
You can view it here...