The point of ettercap is to put yourself between the user and the gateway. Essentially, ettercap turns your machine into a "poor man's" gateway (it's a simplistic way of thinking).
In your setup, you don't need to run ettercap. You're already the gateway. Simply setup the iptables / ebtables to locally terminate those connections which you're interested in. Running Ettercap (or arpspoof, et. al.) may cause weird issues with arp / mac tables.