It's a metaphor. A "boat", as you probably know or could look up, is a vehicle for travelling on water. A boat can carry passengers and cargo. So the writer is saying that punctuation should not be the vehicle that is used to deliver the message. His point is that punctuation should be used to enhance or emphasize a message, but understanding of the message should not rely on the punctuation.
Frankly I think the metaphor is weak. In a well-crafted metaphor, he would have compared what he thinks punctuation SHOULD do to something to do with a boat, as well as using a boat to illustrate what it SHOULDN'T do. The metaphor is just tossed in there as rather an afterthought.
One could also debate his fundamental point. Changing punctuation can and does change the meaning of a sentence. I am reminded of an incident years ago when a political party here in the U.S. was preparing a statement about their policy positions. The first draft included the sentence, "We are opposed to any tax increase which would harm economic recovery." Then they amended this by adding a comma after "increase". I recall that at the time school teachers all over the country used it as an example of how you must watch your punctuation carefully: that one comma radically changed the meaning of the sentence.