I placed wonder board on the floor the flange for the toilet is about 1/2 above the floor tile is this too high and what would be the hight of the flange normally

Should be OK. Sit toilet in place, if toilet sits firmly on the floor, no rocking, you are OK.

Flange can be flush with the floor or the bottom edge of the flange evn with the floor surface. I am thnikning your 1/2" is going to be a bit too much.

The bottom of the flange (underside of flange rim) should be flush with the floor. If you tile the floor be sure that the top of the flange is not lower than the finished floor. Be sure that the flange is securely screwed/fastened to the floor so that it does not move.

Just reread your piost, are you planning to tile on top of that wonderboard. If so you should be just about perfect, the toilet sits on top of the tile, you would not want to tile around it so this should work out