Can I do this and not wear out my clutch and/or manual transmission?
Instead of pushing the clutch to downshift when I am coming up to a red light, this is what I do. I shift to neutral without pushing in the clutch and glide to stop. I started doing this so I wouldn't be pushing on the clutch all the time to downshift. Is this OK or not? I have a brand new 2010 Kia Soul. When I went in at a little over 3000 miles for the oil change, they said I was using the clutch too much. So great I've had it 3 months and it's already wearing out?

I assume that they are referring to an unduly worn clutch plate. I'm not a car expert, but I can't imagine what you can be doing to use the clutch "too much" if you are simply using it to shift gears. I have a 5-speed Saturn with over 140,000 miles in mixed traffic and it has the original clutch. Unless the Kias are really behind the times or it is a wildly poor design (both of which I doubt), your clutch should not be wearing out for a long time.

Could it be that you are driving with your foot on the clutch all, or a large part of, the time? That is called "riding the clutch" and is a no-no.

That's what I was thinking. Also, the long delay in getting the vehicle rolling. Some drive way too much gas and ride the clutch pedal too long. This will wear it out way prematurely.
If you're getting used to shifting into neutral while rolling to a stop, think of this, down shifting and letting the engine do the braking save tons on brake parts.
Never put too much force on the transmission trying to shift without clutch. It puts a lot of pressure on the synchronization. If you become very good judging engine rpm and speed to let it slip into neutral without force, then it shouldn't hurt anything. Just 2 cents worth. Happy driving.

One more thing to ponder... if you downshift when you come to a stop rather than putting it into neutral, you're actually saving gas (counterintuitive, huh?) It's because the momentum of the car keeps the engine running rather than the gas itself.