After a bit of googling I have learned that I can do the following
Delete[domains, Position[domains, "aa.com"]]
However, I think this only works if the element exactly matches the pattern, so my revised question is how would I search for a substring within an element. In effect I want to do something like this
Position[domains, StringMatchQ[#, "aa.com"] &]
But I can't quite work out how to do this.