Card-present transactions are typically cheaper, because the risk of fraud is better mitigated. With chip cards, the fraud risk for card-present is almost entirely in physically stolen cards. (Sophisticated shops could duplicate magnetic stripes. That's a lot harder to do with chips.)

Compared to online, where all you have is the card number and the CVV, both of which are easily duplicated. And this is why tokenization is such a big deal. Tokenization means you don't store the actual card number, and the token you do store is tied directly to your merchant, so it's not widely reusable.