As someone who has been involved with the regulations on sulphur emissions from ships since 2004 I have to say the author has rather missed the boat (insert bad pun groan here).

Exhaust gas cleaning systems can be installed on ships to eliminate the sulphur and dramatically reduce the particulate matter allowing the ships to use cost effective heavy fuel oil (HFO) 

The alternative is to refine the HFO into diesel fuel. This. however, creates additional CO2 emissions, has a significant cost impact, and does little to reduce the most harmful sub 5 micron particulate emissions. 

The technology is relatively new and is installed on only small part of the commercial fleet. As it matures, additional PM, NOx and CO2 reductions will be possible. 

As for the 1000's of cars emissions comparison - this is a misleading statement at best.  How many pickup trucks would it take to deliver grain from Thunder Bay to the global markets? Several thousand. I have a much better idea, use a ship.