Reasons to trunk a story:

1. If it were published you wouldn’t tell anyone and you’d hope no one would read it.
2. You know it’s not together yet. Parts might be working, but parts aren’t. It will simply accrue rejections and thereby limit its markets for when you do figure it out in the future. Put these on the trunk’s top shelf. Months from now you might know exactly what needs to be done with them.
3. You’ve seen hundreds of stories exactly like it in the slush and yours isn’t any better.
4. Better a story go in the trunk then e-pub it and guilt all your friends into buying it.

With the caveat:

NEVER THROW ANYTHING OUT.