Because the sea is cruel. People go out to sea and don't come back. In polytheistic religions people try to find meaning in natural misfortune by blaming cruel gods. And they try to avert misfortune by appeasing the god with sacrifices.
If the god of the sea was good no one would ever drown.
It's established that prestesses of Umberlee are seen as a necessary evil. They are not popular but it would be stupid to go to sea without making a sacrifice to Umberlee first. But in terms of the narrative Umberlee is more usually background colour than antagonist.
You certainly could say all gods are unaligned, but that's pretty much the Eberron solution - you are saying the gods are impersonal forces, not beings with personal volition.
What you decide for your own setting is up to you, but it's already established that the gods of FR are not impersonal forces, just like PCs they are individuals who can make moral decisions, so they have to have alignments. And those alignments are symbolic of what they represent: the Sun is good, storms are chaotic, judges are lawful, etc.
D&D certainly isn't going to make a universal ruling that "gods cannot be good" because there are an awful lot of real life religions that would take exception to that, and WotC do not want a rerun of the satanic panic.