We have a courtesy tone on the repeater here because we find it helps new users understand that they reached the repeater, and don't need to keep asking "Is anyone hearing me on the repeater?" Some users still have their roger beep on, so you get a double tone every now and then, but it's not a huge deal. This is because a lot of users also talk on simplex, and they like to have the beep on.
If this was on more radios, that would definitely help our double beep "issue".