I've airbrushed tiny gingham checks on fondant using tape. It was tedious, but it worked well.
To prevent the tape from sticking to the fondant too well, I pressed it on a kitchen towel a few times to remove some of the adhesive, then taped the stripes.
To do the gingham, I had to remove the tape, give the fondant a half turn, then reapply the tape and airbrush again. Yeesh. Now, I just use edible image gingham. LOL
Anyway, the tape worked great. You'd want to roll out the fondant a little larger than you need so you could trim off any messiness on the edges.
I agree with Texas Rose regarding placing the alternating colored stripes on a fondant backing. I've done this many times and it works well. Be sure to glue the stripes to each other as well as the backing so they don't come apart while you're arranging the flag.