This is not increasing the percentage-based cut (referral fee), this is increasing the fulfillment fee which is size/weight based.
(I.e. what you're saying seems to be that for a $100 item that they charged $5 to ship previously, they will now be charging $5.25. Hard to complain about that.)
An example they give is of a small, standard 6-oz package where the fee will increase from $2.92 to $3.07.
[0]https://sellercentral.amazon.com/gp/help/external/GABBX6GZPA...