If you want to make a selection transparent, just hit [delete] (or Edit>clear). If necessary add an alpha-channel first (Layer>Transparency>Add alpha channel)(*).
Color-to-alpha is not meant to make things completely transparent. It erases the specified color, and leaves the rest. So if you have a purple pixel, using color-to-alpha to erase the ted leaves you with a partially transparent blue pixel. And if you insert a layer under this and fill it with red, the partially transparent blue over the red will reconstruct the original purple.
(*) If you are still on 2.8, C2A adds an alpha channel automatically, so it seems to solve the problem. But on 2.10
this is no longer true, you have to add the alpha channel yourself anyway. Two hints:
- Gimp doesn't add an alpha channel when loading from format with no alpha channel (JPG, typically).
- Layers without an alpha channel have their name in boldface.