There are two ways one arrives at the idea that this is acceptable and should be done:
1. (The one the paper discusses) Newborns with serious health problems, that if left to live will be an enormous burden on their parents, on society as a whole, and, in the end, on themselves too, usually without being able to contribute much to society in any way due to their mental disabilities. Related to this is the eugenics argument - we can in fact eradicate a lot of Mendelian disorders that manifest only later in life such as Huntington and improve the gene pool of humanity as a whole if we did not let the newborns with such diseases reproduce (which now, with whole-genome sequencing about to become a routine clinical practice, is entirely possible). The problem is eugenics has become a dirty word due to the totally misguided way in which it was pursued back in the days and together with it the very rational core idea behind it.
2. Overpopulation. This is more heinous than the first one because the reason why the problem of overpopulation dictates the acceptance of the practice of infanticide is that humanity as a whole has to stop its individual members from reproducing if humanity as a whole is to survie, but the most fundamental biological instinct of individual members is precisely to reproduce as much as possible. This means that both state-mandated forced abortion and state-mandated forced infanticide will have to be implemented if we are to seriously tackle our ovepropulation problem, i.e. we will have to change our socially accepted moral code in such a way that infanticide for surplus newborn babies is seen in a similar light to how penalties for tax evasion are seen today.
Note that the above are conclusions that inevitably follow when one thinks about the issues in a emotionally detached way. They are horrifying conclusions, no doubt about it, but the universe has no obligation towards us to maintain our emotional comfort, it is what it is and we have to adapt accordingly.