The editors of literary magazines--places where short stories are usually published--tend not to make big profits, if any at all. That's actually an advantage for us writers. First off, people who run lit mags aren't just trying to make a buck. Most of the time they are in it because they want to help promote writers and writing. That means terms like "marketability" are not calculated into their acceptance decisions. Also, the people who run these publications tend to be other writers, rather than agents and editors. Again, for us, I think that means the art side of the writing will be emphasized over the profit potential.
Whether you are self-publishing or publishing through other means, having accessible short stories helps to build your platform. Readers, agents, and publishers who are unsure of whether or not your stories have an audience can at least see that other people already love your work enough to make space for it in their journal. And, your ability to get published sort of snowballs as a result. Whether this system is fair or not, the more publications you get, I think the more publications you are capable of getting. The people who make it their job to judge writing, often rely on other judges before deciding if your writing is worthwhile.
For a discussion of whether or not you should send your stories to online publications or print publications, check out this old post.