The engines are really efficient. Unfortunately, the cheapest fuel has a lot of sulphur in it, so there's a lot of sulphur dioxide that comes out of the engine. Low sulphur fuel is 4x the cost.

So, yeah. I don't think the cargo ships are villains or anything, but one of them is worth 50 million cars, for that specific type of emission. (cars would be higher, but they're regulated.). Generally it's turning around, different countries are requiring low sulphur fuel, in spite of the cost. The us was January, i think.

The problem is the fuel itself, as long as you're in international waters you can use as sulphur-rich fuel as you like. Sulphur rich fuel is the cheapest of the lot and because it has no other uses beside international water fuel for freighters, this shit accounts for huge percentages of sulphur emissions.

edit: Reason for this is that burning sulphur in fuel produces sulphur dioxide, which when combined with rain or natural humidity, makes acid rain.