If your religion/religious text were true and could actually provide evidence that it is true, do you think it would need to threaten people for not believing in it? This is a key difference between religion and math/science. A mathematician uses facts and logic to prove statements, a religious person uses threats of eternal torture. What would you do if your math teacher said that the square root of 2 was irrational because he said so and told you to just shut up and believe it because you'd be sent to hell if you didn't? You would laugh in his face. Mathematicians and scientists don't have to threaten people to demonstrate that they are right, instead they use facts and evidence to backup their claims.
I see what you are saying.
I think the way it should be humans all agree upon proofs of religion as well. However, when it comes to God and religion, we are more insincere and even to a degree stubborn.
Let's take away the issue of hell for disbelievers in Messengers for a second. What if there was hell regardless, should God warn about it? I think he should.
It seems you have more of a dispute with why disbelievers are going to hell and why they are threatened. The Quran says whether warned or not warned, they won't accept. So it's not to convince the majority of them. Quran acknowledges it won't work.
However, there is a verse that says that pious of bani-Israel (children of Israel) were asked why they warn people they know won't listen and continue to disobey, they said, for (1) to be free from blame (2) that there is a chance they may fear God.
Although little chance, the chance is there.
God is trying to salvage what he can of humans and jinn.
Then comes the question, okay hell for evil people, but why are disbelievers deemed evil per Quran. And it's not simply for rejecting truth but that truth has proofs and is manifest to a great degree (and hidden to a great degree).
I see this for example with regards to Imam Ali (a). People when they hear proofs whether in hadiths or Quran, they turn aside.
So it's not just atheists.