A cover letter is certainly the norm. It’s a way to introduce your intentions in submitting the story and to say a bit about your writerly biography. Cover letters are best kept short. They don’t take a lot of time and they communicate a great deal about your professionalism, your investment in your work, and your willingness to engage in the process as it exists. The information found in it may also land your manuscript in the pile that gets a quicker read. They take so little time that it seems the message you send with the inclusion of one far outweighs any drawbacks in the preparation of it.
That being said, skipping the cover letter isn’t necessarily an automatic rejection. It may be at some journals, depending upon the editor’s ideas about the importance of the letter, but it may not be at others. Skipping the letter or preparing a perfunctory one that simple says “story attached” does lend insight into what it might be like to work with you. Make sure your manuscript package sends the message that best reflects who you are as a writer.