We publish between 70-100 writers every year, and we pay every single one of those writers; reading fees help offset that expense.
We like to pay writers more when we can, so we often run essay contests (with prizes ranging from $1,000-$10,000 per winning piece); reading fees help us offset that expense.
Submitting work online is incredibly convenient for writers, but in some cases, it can be too convenient. Charging a nominal fee helps eliminate spam submitters–and it helps offset the administrative expenses of processing submissions.