My response to your first point was going to be "that's why you have to build the airport first" which is exactly why your second point is what it is.
It's probably not fair to let a city build up then plop an airport right next to a bunch of houses, marginally increasing their value to a vanishingly small minority of people for whom living near an airport is a plus and cutting it in half for most other people. But this is why eminent domain is also a thing - sometimes you just have to do it. The problem with airports specifically is that you'll get people from miles away who realistically will feel no ill effects complaining about it as well.
It's probably not fair to let a city build up then plop an airport right next to a bunch of houses, marginally increasing their value to a vanishingly small minority of people for whom living near an airport is a plus and cutting it in half for most other people. But this is why eminent domain is also a thing - sometimes you just have to do it. The problem with airports specifically is that you'll get people from miles away who realistically will feel no ill effects complaining about it as well.