When I set the alpha value of gl_FragColor to 1 here is the result.
However if I set it to 0.5 thats what I see, but not anything transperent is this normal?
Have you enabled alpha blending in your renderer?
glEnable(GL_BLEND);
glBlendFunc(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA);
More meaty stuff: Tutorial 10 : Transparency