A lot of indie comic folks complain about fan art, and with good reason. With a set amount of dollars available at a given convention, you want as many of those dollars to flow to your table as possible. However, that's pretty hard to do when you're up against Naruto, Justice League or the Avengers. There's been plenty of videos and forum posts discussing how much of a supposed cancer it is on the independent scene and the comic convention scene.Fan Art detractors say that it goes against the spirit of comics, they say it clogs up artist alley, and they even say that artists who traffic in fan art are thieves that will soon feel the wrath of the huge corporations they "steal" from. Despite this, fan art continues to not only grow, but thrive on the convention circuit. Like an sinister virus, the use of fan art to generate profit has risen exponentially over the last few years, and even correspond with the rising table costs of many larger shows. As more artists dip their toes into attending conventions around the country, more are choosing to draw fan art in order to come out even or ahead of their ever increasing convention-going expenses.
Since it is apparent that fan art isn't going away any time soon, and since independent projects need money to thrive, I would argue that you should merge the two together. In short, set up fan art and use it bring people to your table and then convert those people to your indie project. In my experience, consumers who are already attracted to your work are more apt to purchase something a bit more special or personal to you as the creator. Oftentimes, this appears in the form of personal art (commissions) that are often times priced far above the base price of fan art prints. Not only could you potentially convert these customers over to your comic, you could offer your comic for free alongside a large purchase that didn't cost you much money.
For example, if someone comes to your table and buys 7 prints, just throw a book in the mix. Considering the extremely high profit margins that prints provide, tossing in a book won't hurt you much, will delight the customer, and more than likely create a new fan.
Obviously this works best for a creator who is also the artist of a book. Unfortunately I don't have much advice for people who are writers only beyond simply keeping at it, and don't get discouraged. Independent comic publishing is a rocky road for all of us.
