You know when I started out I didn't understand exactly what a treasure hunt looking for a market can be. In my naivety I thought it was simple, write a brilliant story or book, send it out to the publisher of your choice and viola! A published manuscript would appear. :-) Ha I say, HA!
Any number of things can keep your brilliant piece from being accepted at one place or another. Maybe the imagery is too intense for that particular magazine, perhaps the brilliant plot twist you had was similar to one recently acquired by the magazine, maybe the thing just doesn't tickle the fancy of that particular editor that day. Heck maybe it just really isn't a good fit for that one magazine or anthology. Anything is possible.
But don't give up! For heavens sakes don't give up. For all the reasons that your story may not be accepted the same amount of things can get your piece accepted. then sometimes you look and look and just cant seem to find a market that fits your story. Good News! there are ALWAYS new markets coming around.
Case in point. I've wanted to write a story for a while now about someone with the same religious background as me in a purely speculative fiction setting. I haven't done it. Why? Because frankly the places I've seen that take speculative fiction generally frown on having religion as a core point in it. And the places that take the Religious stuff don't take speculative fiction. I thought it was a waste of my time to write it.
Then last night, looking at markets for a totally different story of mine, I ran across an anthology taking subs for EXACTLY that! I AM SO EXCITED!! I can't wait for another few hours to pass so I can tell a friend of mine who I know has been looking for something similar.
So don't give up. If something you have isn't getting accepted, keep polishing and keep looking. It's just a matter of time till you find that right market and get that acceptance letter. And share those markets my friends. If you've been looking for them then someone else has too. and if you dont already have these websites book marked I highly recomend doing it. Duotrope and Ralan's make market research so much easier.