The way I see it: The comic strips are totally free. The plug didn't make the strip less funny. You're still free not to use the promoted service. Not much worse than ad banners, and surely a legitimate way of earning money.
Come on, gang. At least he doesn't have to worry about getting sued by somebody else for making fun of THEIR website that just happened to have the same URL as what Scott chose. This way, if nothing else, he can sue himself.
What a shameless plug for your other business! The comic would have been just as good without mentioning dilbertfiles.com at the end (and everyone probably would have guessed he was referring to dilbertfiles.com) because I've worked with people who started businesses like this when they had nothing to do at their current employer.