IMO, the sport/activity you are going to be taking part in, along with training history, injury history, and current physical capabilities all are factors in determining what is appropriate for exercise selection, etc.
What I am not fond of in the article is how they made blanket statement against exercises for all athletes. From my experience working as an athletic trainer for a variety of athletic settings, as well as an athlete myself, I agree with their recommendations when they are pertained to track athletes, whose hamstring injuries commonly come from over-training, fatiguing of the hamstrings. Specifically with track athletes, I would recommend a decrease, but not complete elimination, of knee flexion based exercises.
When it comes to multi-directional athletes (american football, european football/soccer, rugby, etc), along with hamstring injuries, there is also a great concern for ligamentous structures of the knee. The ACL specifically is protected by the eccentric strength of the distal hamstrings (amongst other factors), so to avoid training the distal hamstrings would not be beneficial to those athletes. Again, the amount of training would be dependent on the athlete's current strength and injury history, as well as their position in their sport.
Another factor that I have noticed a lot from my experience is that people with chronic hamstring strains have almost always had poor gluteal activity and control, and poor hip mobility, along with tight, restricted IT bands and/or adductors. Specifically with tight IT bands, you will have and increased demand placed on the biceps femoris, which is what the article stated was the hamstring muscle with the highest injury rate. If there is weak/inhibited gluteal function, than the hamstring will have to take on the extra load that the gluteals are not taking up.
The article also stated that "Poor timing-intermuscular coordination and eccentric strength in the short head of the biceps femoris muscle". But the short head of the biceps femoris has no ability to extend the hip and is mainly responsible for flexion at the knee. So to bastardize the knee flexion exercises, but claim that the short head of the biceps femoris has poor timing-intermuscular coordination and eccentric strength doesn't make sense to me. Maybe I am mis-interpreting what the author was trying to say in the article, but if they are stating that high rate of hamstring injuries is due to short head of the biceps femoris, then I think proper training of that specific muscle would be needed.
I guess I will refer to the old adage - You don't need to throw out the baby with the bath water. Majority of athletes will benefit from more hip extension based exercises, but that doesn't mean that they all need to eliminate knee flexion based exercises.