Card-not-present costs more, for a reason
Without the card physically present, the fraud risk sits with you rather than the terminal, and the pricing reflects it. If your online rate looks worse than your in-store rate, that is why.
It also means a single blended rate covering both channels is rarely competitive on either. See them quoted separately.
You may be paying for a gateway twice
Online acceptance usually involves a gateway presenting the checkout and an acquirer settling the funds. They can be the same company or different ones, and each can charge you.
Merchants regularly pay a standalone gateway fee long after moving to a platform that already includes one. It is one of the more easily recovered costs on an online statement.
Chargebacks are the cost nobody quotes
Every disputed transaction carries a fee whether or not you win it, and a high dispute rate can affect your pricing or your facility. Ask what a chargeback costs and who handles the response before you need the answer.