When a seed germinates in has to rely chiefly on its stored energy to pop its cotyledons above ground. Germinated seeds have to draw water to use this energy. When the taproot (little white stub that pokes out of the seed) cracks the shell and grows outwards, it immediately grows root hairs to absorb water. Root hairs are not visible to the naked eye, when you pull the seed from the paper towel and drop it into the ground, you tear off the root hairs that are on the paper towel.
Taproot regrows root hairs usually, but when it can't. . . thats when the germinated seed dies below ground. Sometimes medium doesn't stay warm enough or the proper level of moisture to properly stimulate the seed to begin growing its taproot and your seed molds below ground. I've had the best experience with rapid rooters (root riot cubes probably work just as well) because it keeps the seed at an excellent level of moisture, warmth, etc. Additionally the pre-punched column in the rapid rooters is a little looser than the soil around it and the seed pushes up that much easier.
Did I mention this is what Subcool uses? Won't affect yield or end plant size, but moving seeds around or having them work harder to germinate wastes time and you'll have more seeds die on you. I'll never go back to paper towels or soil ever again. These things kick ass baby.