It's true that so far every step of the way we have found environmental factors that are generally in favor of life. However, there are still many factors we don't know anything about. Somewhere between the possibility of one of these remaining factors being extremely unfavorable to life and us just being in a very isolated location, there should be an explanation for the Fermi paradox we're actually experiencing.

Sensationalist title aside, the article actually plays it extremely safe, by asserting a very high probability of extraterrestrial civilizations having been existed somewhere in the past.

But even so, there are potential problems where that might conflict with observation. I'm not generally a fan of these "alien civilizations must construct huge machines and must have a huge energy output" assertions, however, all it would take is one of the previous civilizations to have built something we can recognize. Sadly, nothing has been found, neither artefacts such as probes, nor radiological evidence in the sky.

Now, there are many possible reasons for why we haven't found anything yet, first and foremost being that the galaxy is vast in both time and space. But if I forced myself to be especially pessimistic, I would say that the probability of abiogenesis might be way smaller than even our bleakest estimates.