I feel so sorry for you.
Don't feel bad for certain things, like not kissing/hugging someone with stomach flu. It's just good sense.
My friend picked up a stomach bug on a weekend trip away and we were meant to share a bed together, she thought absolutely no less of me when I said, 'it's probably better I sleep on the sofa instead, give you some privacy', in fact she was greatly relieved. Most people don't want company when they're in that situation. They want to be left alone.
If you visit your boyfriend, just remember you can't contract the virus unless you digest it. That means literally sucking your hands, sticking them up your nose and/or eating something without washing them.
If you really can't go, make up for it by calling him and texting him often. Buy him a box set of dvd's online, send a card, use a webcam to chat. You can still let him know that you love him and care about him but it's a phobia preventing you from being there. If he knows you're doing everything else you can he'll understand it's not down to a lack of sympathy.
In terms of worrying about the future, think comforting thoughts such as, I will get a place with a spare bedroom and atleast two bathrooms. Also you now have the time to seek help to overcome your phobia.
Good luck, you're not a bad girlfriend. Putting it into perspective and relating it to another phobia also helps, for example, if you're terrified of spiders no one could call you a bad person for not visiting your boyfriend if he said there was a tarantula running around or he had a spider infestation - that sheds a new light on it doesn't it?! :-)