What you are seeing may not be algea at all. It is probably a fungus growing under the liner.
You can treat it by liberally appling cuprous ferric oxide around the edge of the pool and watering it in well. It can take weeks or longer before you see results.
Super-chlorination or shock chlorination can bleach the rust color out, but will not kill the fungus under the liner. A copper-base algeacide may help, especially if it contains silver too, but don't pin your hopes on it.