We are asking who you would like to pay transaction and merchant fees. Message Blocks collects 2.1% of all transactions. Stripe also charges a fee for processing credit card payment, they collect 2.9% + $.30 per transaction.
When you choose "We pay transaction fee" these additional fees do not show up while your attendees are registering, and the fees are collected before appearing in your "Payment" section.
When you choose "Attendee pays transaction fee" the additional fees will appear as they checkout, listed as "Fees" above the total.