I have a customer that has a domain registered via register.com and there is a huge add at the bottom of his site. any ideas on how to get rid of this?

yes, transfer away to another registrar or have them not use register.com nameservers

default nameservers of register.com shows the banner ad all the time (if they use forwarding or any of their free services)

best thing to do is use another nameserver besides register.com's

Transfer to somewhere like eNom or DirectI.

You can use DNS services like zonedit since I do not think they use banners ads on their service.