It would depend on how big the holes are. I have used some fiberglass stuff called "Kitty Hair" to patch some small holes, and it has worked well. I am not sure how large of an area you would want to use it on - I have never used it on any hole larger than 1" - 1.5".
I have to say most people do NOT recommend it. It seems whatever is patched always comes loose later. I you use bondo to patch rust, I guarantee it will fall off later.
All that said, I've had good results patching small stuff with fiberglass. Fiberglass (unlike bondo) can be waterproof if correctly applied. I used to know a guy who made a huge patch on the rear of his old Duster quarter panel. It had to be at least a foot square. He actually did a very good job with it but never bothered to paint it. Weird guy. I saw him and his Duster around for 10 years. The rest of the car slowly fell apart but that quarter panel stayed solid as a rock.