I've never had any problems using the paper towel method. In fact, I've had better results using that method, rather than sowing directly into the soil. I think this might have to do with the viability of the seeds themselves. If the seeds don't crack and shoot out a taproot in the paper towel, then it's unlikely that it's going to do any differently in the soil. This gives me a chance to weed out the weak or sterile seeds, and replace them with seeds that are sure to germinate. By the time I transplant into soil, the taproots have already broken the shell, and give me an almost 100% guarantee that they'll make the transition from ungerminated seedlings to sprouts.

Use whatever method works best for you. Just don't disregard one method for another just because someone else may have screwed up and killed the seedlings before they ever had the chance to transplant them. There's no right or wrong answer here...do what feels most comfortable to you.