There are some good reasons to submit to literary magazines published by MFA programs. These magazines are run by enthusiastic students and their professors, which means they are more than happy to nominate the stories they accept for Pushcart and other national prizes. They are also read by faculty and alums, which means any agent or editor who has graduated from an MFA program (and there are quite a few) will see your work. (I know of at least one person who secured a publishing contract based on a short story that appeared in an MFA literary journal.) Here is a list of 130 journals accepting submissions. Twenty of them pay; 76 of them do not charge submission fees.
Publishing ... and Other Forms of Insanity: Mega-List of University Literary Journals Accepting Submissions in Fiction, Poetry, Art, CNF
Publishing ... and Other Forms of Insanity: Mega-List of University Literary Journals Accepting Submissions in Fiction, Poetry, Art, CNF