I consider them to be different: trawling is dragging a net through the water, while trolling is dragging a baited line through the water.
Wikipedia seems to agree with me, but I have no access to OED until tomorrow so the irrefutable argument from etymology will have to wait :)
As an aside: in my NZ pronunciation these are quite different words, and I’m curious as to whether they are homophonous for those poor souls amongst us who suffer from the “cot/caught” merger?