Unless your roger beep is the dtmf tones to 'mary had a littte lamb', its not likely going to cause problems.
As a radio user (ham, gmrs, frs, muuuuuuuurs, cb), I don't like the actual tones of the boofwang radio roger beep, but I do prefer a roger beep when talking to someone, especially on simplex. On weak signals if I don't hear a beep I assume they dropped out and will come right back. If I hear the beep, I know they released the ptt. Otherwise, you just talk over them, which happens frequently on 2m simplex or repeaters.
Sad hams just don't like the roger beep.