It has to do with its positioning within the legacy of the park, and therefore the Walt Disney World resort as a whole.
As the original Icon of the Studios, many guests who visited in the late 80's-most of the 90's connected with it as a significant structure within the property and a symbol of Walt Disney World - one that, despite losing the title of official Studios Icon, retained its emotional charge with that group of guests by remaining in the park even as the "World" changed around it.
In a park that's been grappling with an identity crisis for the better part of 15 years now, it's stood as a symbol of what was when that park was decisive, and a reminder of a time where things were looking up for the resort. After 27 years, it makes sense that to many it is no longer just a "fake water tower", much in the way that Cinderella Castle is not just "a fake castle". It means something when you see it - for many, seeing the Tower was part of coming home to the place they grew up.
That place has been changing for a while now, but the Tower was always there. It makes a statement about the park to remove it, and while it's probably a sign of great progress it does also mean letting go of part of "home", and that's not always easy.