Magazines mostly take online submissions...correct that...some of them do. Each magazine's site has different rules. Gotta upload it as a rtf file, a doc file, a pdf file, or as a text file. No standards. In the old days, there were simple rules for producing a manuscript that everyone respected. Editors online will even require one font over another, or ask the writer to convert the work into an e-reader format.
Gotta put up with it. I make it sound like a great burden when it's only a mild annoyance. After the first few times, it becomes easy to do.
One thing I miss from the old days - I say old days, I mean fifteen years ago - they always told you if they rejected your story. Now, silence. A few will send a canned email response.
But a few things stay the same. The short story is still a dying art form. You'll be paid by the magazines at the same rate Harlan Ellison was paid in the 1960s. So it's a joke. Write short stories for yourself, for fun, not for any commercial purpose.