It might. Especially if it's a rubbing compound that has waxes and whatnot in it to create a "glossy shine". These waxes will adversely affect the art's ability to adhere.
So you should try and find a rubbing compound that doesn't contain any waxes or "shine enhancers" in there. I can't think of any off the top of my head right now.
Another thing you can do is after you have used the rubbing compound, get some mineral spirits or 95%+ alcohol and rub down the area that the artwork will stick to, and ONLY the area the artwork will stick to. The mineral spirits and/or alcohol will probably not be very friendly to the paint, so you only want to do this where the artwork will cover up the 'damage'.