Programs wouldn't really have any way to know where you rotated, except by assuming from LOR's and you telling them. Regardless, I wouldn't worry about it. Rotate where you're interested and leave it at that. That being said, if you're from the NE (for example) and really want to head south, you may want to rotate down there.

I did both aways in NYC (with letters of rec and grades included on my deans letter), and was able to get interviews at nearly all Boston and Philly programs, 2 Chicago programs, but only 4 NYC programs (and I applied to all of them). Go figure.