Yes, you should. Your presence there is about paying your respects to your deceased friend. It is not about making a statement. Also, remember that it is HIS minister, not yours. Go to the service, be respectful, comfort the family and pray for the repose of his soul. Participate in the service to the extent that you are able to in conscience. Most Protestant traditions do not offer communion at funerals, but if they do, politely decline as it would be dishonest to participate in communion with a church with whom we are not in full communion. The best thing to say to the family is “I am very sorry for your loss.” Remember, at funerals the family will seldom remember anything you said, but they will never forget that you were there.