Yes, I know, and I addressed that.
Since your meat is "fixed" at level 1 (you don't "grow more" or "better" meat as you level, obviously), all that is left to increase with level is your ability to endure fatigue. Why would your ability to endure fatigue (which is just another way of saying endurance - they are synonyms) go up as your level increases? It might make sense for a fighter who swings their sword all day long, but for a lot of classes, why would their ability to endure fatigue increase as they overcome challenges?
Do not think of it as gaining an increased pool of endurance as you level. Instead think that you are becoming more effecient at using your existing body. If you are skilled enough, it takes you less enerfy to roll with it when you are hit by the ogres club. So your HD represent your short term fatigue and ability to completely avoid attacks through dodging, blocking, and parrying, your HP represent your ability to turn great wounds into minor scratches or to otherwise take a hit.
This is why when you take HP damage you still only suffer scrapes and bruises instead of having your limbs chopped off. Another good module to this would be that whenever you suffer HP damage greater than 1/2 your Max HP (after reducing it with HD), you will suffer a major wound.