Like I said, it should just do it automatically. It does for me... I can take any targa and just load it into Maya as a file texture and the transparency is clearly visible. I even tried this again just to make sure.

WHen you go to your material's attributes, make sure both the transparency and color are mapped to your targa file. If they are and it still doesn't show, try clicking on the checkered box to the right of the transparency slider to bring you to the transparency thing. Look under the colorBalence tab and play with the Alpha gain making it 0 or -1. If THAT doesn't work, try setting the Alpha offset to 1 or -1 with Alpha Gain as -1 0 or 1. ONE of those HAS to work if the alpha gain/offset thing is your problem. =P

If you still can't get it to work, I have absolutely no idea what it is. If I had a guess, I'd say that you did something wrong when putting the alpha layer in your image to begin with.