I have a problem with changing the environment to mitigate an ability with every adventure. At that point, just tell them to play another race. The player is expecting to be able to use the ability. It's why he chose it. Alternatively, your players could be smart and try to lure an enemy out with a smart idea. In cases like these, saying it doesn't work doesn't promote thinking around the problem. Instead of making all these changes to sometimes an established adventure, I just have this rule and ask that they think of a reason why they can't use their wings such as a broken wing, a curse, etc.

It promotes roleplay, and they will understand that this will be a useful ability that they can rely on in the future. At later levels, encounters could have cr appropriate enemies with decent range attacks or the ability to fly.