I just tried my first soil germination. I have suspected on several occasions that damage to the tap root while germinating in paper towel caused some issues for a few of my plants, and I also have seen it cause tap roots to grow loops and U shapes before heading down, which I figure has got to be a bad thing.
Like other posters, it's been 3-4 days, and I've already worried about them. But when I think about it, towel germinating I usually see a tap root at 24-48 hours, and then once planted it usually takes a day or three to break through soil, so I am being patient and having faith they will sprout up!
I have been worried with the jiffy pellets that it might dry out, so I have been keeping a little water in the bottom, and the plug has been staying quite moist. I plan on planting as soon as I see the surface break, and will stop leaving the soil wet. I hope this all works, because I like it a lot more than germinating outside a grow medium.