Of course the OP's seatmate has the right to lend or not, and explain or not, but the "Yes I do" response seems unduly harsh. "I'm sorry, but I don't lend pens because I don't always get them back" or "I'm sorry, but this pen means a lot to me so I don't like to lend it out" (unlikely the reason if it was a Bic) might have reduced the OP's surprise. I think "Do you mind if I borrow your pen?" is perfectly polite.
Seth