OOPS! My mistake. Lowering the flaps (or aileron) RAISES the angle of attack of the wing. The centerline of the wing goes through the center of the trailing edge and the center of the leading edge.

If the fuselage doesn't change it's angle into the wind when the aileron goes down, then the wing with the lowered aileron (or flap) has a higher angle of attack and the wing with a raised aileron has a lower angle of attack than they did when the ailerons were centered.

I'm not explaining this well. Just draw a picture of an airfoil with the aileron level and draw a centerline through it.

Then draw it with the aileron lowered with a centerline through the center of the TE and LE and you'll see what I'm talking about.

For a more detailed explanation, see the Gurus in the Aerodynamics forum.