The ad is the third most complained about of all time, says the Advertising Standards Authority.
The passenger received a text informing him of his positive test result minutes before take off at Stansted Airport.
The airlines are calling the government's 14-day policy "flawed".
Airline CEO Michael O'Leary called for the profiling of Muslim men at airports during an interview with The Times.
A quarter of Ryanair passengers said cleanliness on flights was 'poor', according to a Which? survey.
The British pilots' union has accused the airline of refusing to take part in talks.
A second round of pilot strikes is planned between September 2-4.
Passengers say the airline has unhelpful staff and miserable complaints handling.
Ryanair, which has its main UK base at Stansted, will see many of its airports affected ahead of the bank holiday weekend.
The decision comes just hours before industrial action is due to start.