As always, should you have a question about someone's behavior or something that they've said, you really should talk to them about it. You should ask him why he feels you are stalking him. If you feel his concern is legitimate, you should ask him what would make him feel more comfortable around you. If this is his way to not carpool with him, I would take the hint.
Maybe he is actually stalking you and is just projecting his behavior on yours.
Perhaps you should ask him if he is actually stalking you and that's why he brought the subject up.
But try Danae Hitch's suggestion first.
I would tell him the same way you've told us. "I'm not stalking you, I'm carpooling you, I've only had one conversation with you, what is your deal?" If he doesn't want to engage in conversation then the reason he is doing this is because he doesn't want contact with you.
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