Exactly. The "50 million times more" thing is about sulfur oxides emissions, and honestly this number doesn't seem extraordinary to me. Diesel oil and gasoline have virtually no sulfur in them, while the Heavy Fuel Oil (HFO) that powers most ships is about 2% sulfur.
HFO is what's left when all the "good stuff" is extracted from crude oil. This "good stuff" is mostly shorter hydrocarbons such as methane, ethane, propane and butane (gases with 1 to 4 carbon atoms in them), gasoline (roughly 5 to 7 carbon atoms) and diesel oil (8 to maximum 21 carbon atoms).
What's left is an incredibly dirty, viscous, and nearly useless goo (asphalt is one other use, there aren't a whole lot). It still has a high energy density which makes it a decent fuel, but it's so viscous (because it consists mostly of very long hydrocarbon molecules) that you have to heat it up to around 80 degrees centigrade (176F) to even pump it into an engine. It also has high amounts of pollutants, because all the "clean" stuff has been taken out and you're left with all the dirty stuff. It is technically possible to remove most of the sulfur from this goo, but that means refineries would end up with giant piles of sulfur that nobody wants, and they'd have to dispose of it somehow. That's a cost refineries aren't willing to pay, so they just leave it all in to be burned up.
Legislation is being made to reduce HFO use in some heavy traffic areas (such as the North Sea in Europe), forcing ships to switch to clean diesel fuel in those areas. Of course, shipowners are against this because diesel is about 3 times as expensive as HFO. If all the ships in the busiest sea in the world suddenly start burning diesel fuel, you can expect the price to go up for everyone. Which is why we keep on burning the bad stuff.