I wouldn't say I take it seriously, it is just fiction to me after all. However, there are some great stories told in the setting (as much as I love Relic their games are not the best representive of that.... it usually boils down to "Kill Orcs until the real threat, either Chaos, Tyranid, or Necron show up")
It's like anything. Some people will like it, some people won't. One can say the Imperium of Man is dumb. What are the reasons why? They are on the verge of becoming a psychic species like the Eldar. But the Emperor of Mankind already seen that the species of the warp grew from the psychic backlash of the Eldar. It birthed a new dark god. To keep his people from harm, The Emperor tried to stem the psychic growth of his people so there wouldn't be more warp entities from materializing.
WH40k is not a pick up and play thing. From one game in 2004, I constantly read and looked up more and more about the Lore. I like it on those respects. Just like if someone's first experience of Star Wars was the Phantom Menace, they'd probably dislike all of star wars too. It's all about how you're brought in.