The ads are probably laid out that way because it generates better revenue. The design has a small banner ad unintrusively inserted at the top and vertical ads under the comic on the left hand side. Those ads are placed in such a way that your eyes will wander over them while viewing the site. They aren't placed in such a way as to repel you or intrude on the site's content. That's why you don't see vertical ads to the sides of the comic. Instead you have an ad at the top, near the title and some buttons which take you to other parts of the site you may be interested in. As you view these buttons you will also inadvertently see the ad; your brain may pick up on something about that ad that makes you pay attention to it, maybe even click on it, and potentially buy something from the advertiser. There is a similar strategy at play with the vertical ads by the chapter links. Overall it is a fairly clean design that is both pleasing to the eye (of the end-user, you an I) and to advertisers. With this design Tom is able to make a small profit from his comic at practically no cost to you. (Except if you buy a shirt from snorg tees or something)
All said and done, having and viewing an offline archive of your own will be depriving Tom of some income, and if that makes you feel bad you may wish to consider
donating directly to Tom or buying some
hardcopies instead. Just don't distribute your script or archive because that is almost definitely illegal.