Is your project flaming out? Is the excitement wearing off? Are you bored writing it? Maybe it's time to move on. Even if the idea is a good one, you may be bored with whatever you're working on. And that's perfectly OK!
You shouldn't feel guilty for not working on a project that doesn't work with you. Maybe you just need a break. In fact, it's probably the best thing you could do for both you and your manuscript.
Have you heard the quote "No tears in the writer, no tears in the reader," by Robert Frost? Basically what he meant was that as the writer, you have to feel emotion to properly express it through writing. When you feel the emotion, you write with it. When you write with it, your reader feels it.
That being said, transferring your boredom for a project to the reader, probably isn't the best idea.
You may be inadvertently confusing your reader or channeling an emotion that doesn't coincide with your story. No reader wants to be bored reading a thriller. They want to be on the edge of their seat, turning pages like it's a hot summer day and their fan just broke. Romance readers want to feel their hearts bursting with joy and love.
If your manuscript doesn't make you feel these things, it won't work for your reader either.
I don't suggest throwing the story away entirely. Some writers do. Perhaps you may be one. But I keep everything I write, just in case (even if it makes me feel nauseated when I go back and read it years later). You never know when the idea may crop up again, or if a passage was written well and you'd like to keep it.
In any case, when you put aside a manuscript, just keep it out of sight and out of mind until you're sure you don't want/need it anymore.
Sometimes writers get discouraged when Beta Readers don't like their manuscripts. *This is not a reason to dump a manuscript!* This is a reason to take a look at it, get additional feedback, process the feedback in a healthy, non-personal way, and adjust your writing.
The worst thing you could do when someone doesn't like your work is toss it. It may be exactly as bad as they think it is. That doesn't mean the whole concept is garbage. Take the good and leave the bad. You don't need to get rid of it. Just learn from it for next time.
Maybe the whole manuscript needs to be rewritten (I've been there and done that too). Often times, they do. Multiple rewrites need to be done before the finished product. Ask any serious writer. They spend years on a single manuscript.
Yes, it's tedious and disheartening when a manuscript needs a full rewrite. Yes, it's worth it.
It's time to toss a manuscript when you've given up all hope of ever becoming a writer. When you're done. Completely. Irrevocably. Done. And a bitter goodbye that is.
My point is, it's never time to toss a manuscript. It's only time to put them aside every now and then, until you're ready to pick them back up, or until nostalgia hits. They may be crappy, unfinished, and messy, but they're a piece of your life, your time, your effort, your story. And that's something worth holding onto.