Why can't apples make roots? I have apple seeds starting. What do they use for root stock?
They can

Scion or rootstock, they're all apples and all of it came from seed at some point. But since apple flowers require different varieties' pollen to produce fruit, seeds are notoriously unreliable as a means of propagating consistently desirable traits.
When I'm at Fedco I'll ask about their rootstock propagation program. I'm guessing it's done by getting cuttings to take root. But I'll ask to make sure. If it isn't I'm sure it will be something interesting!