Well of course per passenger-mile shipping is less efficient than air travel, because shipping is primarily transportation for goods, not for people. A big container ship has what, 20 people? Nonetheless, you're right that shipping should receive more attention. I think that it's less visible, less profitable, and more economically critical than air travel, which is often seen as a luxury. This would make taxing it more of a tax on economic activity.

Air travel produces a factor of ~100 more C02 per unit mass transported than maritime transport [1].

It seems that shipping is a little understudied, but apparently a leaked UN IPCC report (from 2008, so pre-crash, peak globalization) states that shipping produced 1.1 billion tonnes† [2] of CO2 annually. This number is ~4x higher than other studies so maybe it's more accurate, maybe it's not.

Air travel on the other hand produces 780 million tonnes of CO2 per year [3]. The major issue is that, as stated in TFA, it's supposed to triple in coming decades. I am not sure that global shipping is.

†I am quoting 'tonnes' in both which I think refers to metric tons, not imperial measurements, so I believe the units are comparable.

Shipping may be much easier to improve technologically than air travel, though. I'm sure many of the ships burn low-quality diesel. However, they're of the scale where very small nuclear reactors are available, and I have heard talk of ships being powered by natural gas. Ships can also deal with heavy batteries, so maybe in some instances offshore wind or solar farms could provide electricity? I have also heard of ships actually being powered directly by wind, but maybe this is a rumor, some far off Silicon Valley pipe dream.

[1]: http://www.davidsuzuki.org/issues/climate-change/science/cli...

[2]: https://www.theguardian.com/environment/2008/feb/13/climatec...

[3]: http://www.atag.org/facts-and-figures.html