Homeschooling is terrible, because it keeps the child isolated from the world and thus unable to properly communicate with people and reconcile differences in beliefs, lifestyles, etc. They end up sheltered and ignorant about how the world works. Also, the average parent simply cannot do as good a job at educating their kid as a trained professional can.
I'd say homeschooling probably should not be allowed as an alternative to going to school. It's not true education.
I was homeschooled, and I've never experienced any of those problems. Both of my parents are fairly religious, too. I think you're generalizing.