The idea is that the saying is often misinterpreted to mean that apple pie is as quintessentially American as anything can be, invented by Americans for Americans if you like, where in fact it was something that pre-existed what we know today as America and was something that was brought to America by the people of other nations that settled there, so by saying that something is "as American as apple pie" it's really like saying that it's not really American, that it's origins lie elsewhere.
Something like that anyway.