Yes in some doctors you are meant to pay for the letters, whether or not it is pregnancy related. A doctor writing out a letter for you is something they charge for usually, some you can get away with not paying so i guess some are lucky some aren't & far as i know the nhs exempt card will not cover this as it not classed as a medical expense.
Even if you weren't pregnant & still needed the letter you would have to pay, Again some docs let you off.
Normally one of these letters isn't needed at your gestation unless there are some complications in the pregnancy.
Airlines all vary with rules though so worth checking 1st.