From the "code"
QUOTE
The flag should never be dipped to any person or thing. It is flown upside down only as a distress signal.
* The flag should not be used as a drapery, or for covering a speakers desk, draping a platform, or for any decoration in general. Bunting of blue, white and red stripes is available for these purposes. The blue stripe of the bunting should be on the top.
* The flag should never be used for any advertising purpose. It should not be embroidered, printed or otherwise impressed on such articles as cushions, handkerchiefs, napkins, boxes, or anything intended to be discarded after temporary use. Advertising signs should not be attached to the staff or halyard.
* The flag should not be used as part of a costume or athletic uniform, except that a flag patch may be used on the uniform of military personnel, fireman, policeman and members of patriotic organizations.
* The flag should never have placed on it, or attached to it, any mark, insignia, letter, word, number, figure, or drawing of any kind.
* The flag should never be used as a receptacle for receiving, holding, carrying, or delivering anything.
I particularly like the advertising section. Now, I don't see television very often, but hasn't there been an awful lot of flag-use in commercials in recent years? Yet no one seems really upset about that. As it's just an object with an image on it, I'd say it is in no way connected to your feelings of patriotism. Fly it upside down, write on it, burn it, eat it, dip it in horse dung. None of that stuff means anything at all.
If you want to support the troops and still protest the war, put up a sign saying so - it's been shown, both here on AD as well as in the news, that what you do with the flag is so subjective. Use a sign, say exactly what you mean... that's my advice anyway.