The Payment for Stripe app collects a 1% transaction fee on top of your base Stripe fees for your country. In the U.S., those fees are 2.7% + 5c per transaction (when using the card reader). For example, the fee breakdown would be as follows:
$100 - $2.75 (Stripe fees) - $1.00 (app fees) = $97 NET
These fees are outlined in the App Store description, in the Terms of Service you agree to when authorizing the app to connect to your Stripe account and on our website at https://paymentforstripe.com/#pricing
The fees for the card reader are reduced because you will be receiving "card present" rates (certified with EMV technology) instead of "card not present" rates, which is essentially the rates you would pay to process cards if your business was entirely online.
Essentially, it's less risky for Stripe to process "card present" cards because the physical card is being used.