When you’re training your dog, especially the “come” command, it’s important that he or she feel comfortable coming right up to you. Not all dogs feel at ease so close to someone so much bigger than them (If your dog is huge, you might have the opposite problem!), so they might feel like “come” is a punishment, not a way to a reward.
If your dog doesn’t like being close to you, you need to relax with her more. Dogs can sense when people are angry or upset, and some might want to stay away from that. So play with your dog. Brush him. Give him a bath (but not too often!). Rough house a little with him; scratch his ears, coo at him, encourage him to put his head on your lap or lay across your feet (dogs make great foot warmers!). But no tug-of-war; it teaches bad habits! Get comfortable with your dog. He’s not just the family pet and protector; he’s your friend, and he wants to hang out with you! Let him know you want to hang out with him, too!
Dogs are motivated by food, fear, and love/attention. If you have to scare your dog into doing what you want, there’s an owner issue going on there, not a dog issue. If your dog is only motivated by food, well, be extra careful with how many treats he gets. Too many, and he’ll be sick, fat, or both. Love/attention is by far the best if you get a choice. It won’t make your pup fat, or sick. Showing your dog how much you love him by petting and praising him when he does something right does two things: it builds your bond, and it makes him eager to obey even if there are no treats in sight.