So you can't fit 2 million species on one boat, but a dozen, that's cool? Keep in mind, 2 million, now.
As a matter of fact, yes. There were a number of effects of the impact event, but it's not as if the Earth was engulfed in flame. In a large region near the impact, everything would have been devastated - but beyond that, creatures would have had a chance for survival. The problems for them would include infrared radiation, global firestorms, acid rain, and, most importantly, the particulates in the air inhibiting photosynthesis, killing off plants and those species dependent on them for survival. Some, though not many, species were capable of surviving these effects (the majority of living species died off at the time). We also have plenty of evidence that the impact happened, and that species survived it.
Let us contrast this event with the 40 day flood. The first, most damning statistic is that there's no evidence it ever occurred. Furthermore, it would be far more devastating to life because, as you may be aware, most creatures on the planet like to breathe every now and again. The impact event didn't prevent creatures from breathing (at least, not outside the immediate impact radius). Drowning the world would kill off, well, everything, except species capable of surviving in a saltwater environment and that were able to adjust to the change in depth. Of course, the depth change would have killed off pretty much all of the saltwater plants reliant on sunlight, and therefore everything that ate off them. So, pretty much every single living thing (far more than the impact event killed) would have died as a result of this theoretical event.
In short, a 40 day flood would be far more damaging to the species of Earth than an impact event of that magnitude, devastating though the latter was.
The reason why some species survived the impact event is clear in some cases, less so in others. In particular crocodiles and turtles are a bit puzzling, though there are explanations (I'm not paleontology savvy enough to fully understand). Mammals are easier to explain, since they were tiny and were able to both shelter and survive off the food that was left over.
If you take nothing else away from this, understand how much more damaging a 40 day flood would be to the ecosystem than an impact event was.