There’s not one answer to this question.
To understand why something hurts, first you have to understand what it does. The hamstrings have quite a few jobs.
1. They flex the knee and extend the hip. That is their action.
2. They serve as “the brakes” for knee extension; when the quadriceps contract to extend the knee, the hamstrings slow that motion down as it nears the end of available range of motion.
3. They assist the ACL to some degree. This is important for guys who have ACL surgery and then come back quickly (less than 1 year) from surgery.
So why do we see so many more hamstring injuries today than 20 years ago? Today’s players are bigger, stronger than players of the past. Some of these guys defy human limits, but they tend to find themselves injured a lot (JJ Watt, Gronk to name two). So to point #2 above. If an athlete has massive quads, they need appropriate brakes to slow them down. Imagine driving a semi-truck with Prius brakes… good luck with those brakes lasting. Sure, these guys should work their hamstrings out and be balanced, many do. However, the human body does have limits. Our tissues have a breaking point. So this is one reason; guys are just too big, and often times imbalanced with quad/hamstring strength ratio. This is especially evident in guys who have previous ACL surgery. They are often times very imbalanced. It’s almost predictable that Dalvin Cook is having issues following coming back from ACL surgery. It doesn’t happen for everyone, but it’s the most likely to happen following that surgery. Consider that the hamstrings help with the ACL to some degree. Then you have an athlete coming back after 9, 10 months from an ACL tear. That ACL is not fully integrated yet into the bone and it hasn't turned into a ligament yet from a cellular standpoint- it's still a tendon. Those athletes are going to use their hamstrings a little more and be prone to injury
Often times an injured hamstring takes a long time to fully recover, and not just because of healing time. You have to “reprogram” that muscle how to work. Following an injury, the body learns new ways to move to compensate for pain, weakness, or injury. The body wants to get the job done as easily as it can with the least amount of work or pain. So when you strain a hamstring, it’s healed after roughly 2 weeks, but the aftermath is all what happened during those first 2 weeks: how weak did you get, is it firing correctly (at the right time, the right amount, etc), is it tight/does it resist stretch? This is when you can see guys re-injure themselves easily, such as Fournette this year.
What can be done to prevent this? Well, it’s not just stretching your hamstrings. I remember watching one of Clay Matthews’ work out routines a few years ago and during the stretching portion of his workout he was practically able to get his knee to his face. Yet, that previous year (and the year following this workout) he had significant hamstring issues. So it’s not just a flexibility issue. It’s a flexibility and a strength balance issue, not to mention a running form issue. So let’s talk about that…
Often times, when people are pulling their hamstrings during running, they are over-striding. This puts a lot of strain on the hamstrings for points #1 and #2 above. This is where gait analysis can come in and help athletes, or even weekend warriors, decrease their risk for injury. There is no “magic” cadence for appropriate running form, nor is there a best running form. You’ll hear you should run on your toes, or your heels, or midfoot. Which one is right? All 3; do what works for you. The over simplification of injuries and running is: if you are finding yourself injuring your hamstring a lot during sprinting/running, shorten your stride length/increase cadence and it will improve. In fact, that’s fairly true for most running injuries.
Then the answer that is true for a certain percentage of NFL athletes, and it's using something a little extra to help get bigger, faster, stronger. These "extras" often leave the athlete with weaker tendons, more prone to injury, as well as with muscle imbalances that the body cannot handle. I realize this does not apply to everyone, but it applies to some.
So unfortunately, there is no one answer to the question of why athletes get hurt with hamstring issues. I won't give away all of my secrets, but when I look at guys who might be injury prone I try to look at how they run- do they over stride? I try to look at how they move and see if they use quad dominant strategies. These things will put an athlete at a higher risk for injury. I also look at surgical history- did this athlete recently have a surgery? Was it a long rehab? ACL? What’s the typical recovery and rehab time? I look at injury history too- does he have significant history of hamstring or other strains that result from something more than a fluke? I make a judgement call based on these things. Some athletes concern me more than others. It’s why I disagree with those who label athletes injury prone when really their injuries come from fluke incidents, rather running style or other factors that are more predictable for injuries.