The argument assumes that the only possible end-state for humanity is doomsday; that is, there are a finite number of humans, and when there are no more doomsday has occurred. The article touches on this with the infinite humans / transhuman stuff at the end.
The argument assumes exponential growth in number of humans until the terminal state, but this is not a foregone conclusion. While this doesn't change the reasoning in a strict sense, it may put the "soon" cutoff millions of years in the future.
Finally, the prior probability is chosen arbitrarily. It does matter quite a bit. Take the exponential argument for evidence as to why: For any given probabilty p that doomsday will occur on a given day, it is more likely today than on any single other day! This is simply because if doomsday occurs today, it cannot occur on any future day, making it less likely on each successive day.
Except that if p=1E-10, doomsday is fantastically unlikely to occur this year. The Bayesian argument has the same problem, you just start seeing it at a different value of p.