The most obvious ones I can think of are the Epicureans, who espoused a materialist philosophy. The founder of the school, Epicurus, is credited with codifying the problem of evil, one of the foremost challenges to theism (specifically the proposition that there exists an omnipotent, omnipresent, omnibenevolent deity.) Epicurus lived in the 3rd and 4th centuries BCE, so that's hopefully far enough back for you, although the first written attribution (very few of his own writing survive) is from the 2nd century CE.

The Epicurean paradox is normally rendered thus: 'Is God willing to prevent evil, but not able? Then he is not omnipotent. Is he able, but not willing? Then he is malevolent. Is he both able and willing? Then whence cometh evil?

As I mentioned, very little of Epicurus's writings survived, so there is some question as to whether he actually formulated the problem. However, the best known exponent of Epicurean philosophy was the Roman poet Lucretius, who made several references to antitheist thought in his De Rerum Natura:

'Tantum religio potuit suadere malorum' - So potent was religion in driving men to evil, 'Fear is the mother of all gods' and so forth.

There are other possible candidates among the ancient and classical Greek philosophers - Anaxagoras, Protagoras but the further back you go, the more difficult it is to attribute writings correctly, and I have no expertise on the pre-Socratics. I do think it is safe to say that there was a skeptical/agnostic/atheist line of thought within Greek philosophy, but it certainly wasn't mainstream, and the Greeks were often quick to punish impiety with death.

In China, you have the philosopher Wang Chong (王充, 27 - 100AD), who put forward a materialistic account of the universe. Wang derided the superstition that characterised contemporary Daoism and Confucianism, the then common religions that had in some sense eschewed part of their original philosophical underpinnings and had embraced folk mysticism. On the almost universal belief in ghosts, after flat out asking why it is that only humans have ghosts and not other animals, he rather bluntly states in the Lunheng that, “people say that spirits are the souls of dead men. That being the case, spirits should always appear naked, for surely it is not contended that clothes have souls as well as men.”

Another example of this rationalism is his denial that Heaven, (by which he meant Heaven in the sense understood by classical Chinese civilization and which in his understanding might more accurately be referred to today as the universe,) has any purpose for people, and the insistence that humans are unimportant and that it is arrogance to think that the universe would concern itself with us. Further examples of his thought are the ideas that we ought to challenge the thought of previous generations and that repeatable evidence should be used to explain a phenomena before resorting to divine explanations. He also did much work on meteorology and astronomy, and as you can probably tell - he comes across as surprisingly modern in his outlook. Needless to say, he attracted few followers in China due to his rejection of traditional values, and it is only recently that he has undergone a bit of a revival.

In a much later period, there is Wang Fuzhi (王夫之, 1619 - 1692AD), a materialist who proposed that there are no natural moral values, and that it is human beings who create values. He also stresses the importance of experience and reason in the acquisition of knowledge and that the universe is not composed of transcendental substances. Though he criticised Lao Zi and the Buddha for talking in abstract and extravagant terms rather than concrete ones, Wang Fuzhi was certainly less vehemently against religion than Wang Chong, but I mention him because he is the other main materialist in Chinese philosophical history.

In India there were several schools of atheistic thought. They were called nastika philosophies( literal meaning being disbelief in the Vedantic traditions) . The most interesting being the carvaka school, they shunned the religious texts and rituals as being foolish and espoused materialism. "The Agnihotra, the three Vedas, the ascetic's three staves, and smearing one's self with ashes, Were made by Nature as the livelihood of those destitute of knowledge and manliness"

They believed that all natural phenomenon arise from their own inherent nature and have no supernatural phenomenon "The fire is hot, the water cold, refreshing cool the breeze of morn; By whom came this variety ? from their own nature was it born"

They also believed in sensual pleasure, while the other forms of hinduism were more ascetic

"The berries of paddy, rich with the finest white grains, What man, seeking his true interest, would fling away because covered with husk and dust?"

The brilliant part is that this was not considered irreligious, it was merely another philosophy of religion and flourished with a small group. The philosophers were not considered outcasts.

Edit:- added translated quotes and source. Edit:- typo

sources :- https://archive.org/details/Sarva-Darsana-Samgraha.by.Madhavacharya-Vidyaranya.tr.by.E.B.Cowell

The Apostle Paul kind of implied that smart people would have trouble with religion:

1Cor3:18 Guard against self-deception, each of you. If someone among you thinks he is wise in this age, let him become foolish so that he can become wise. 19 For the wisdom of this age is foolishness with God. As it is written, “He catches the wise in their craftiness.” 20 And again, “The Lord knows that the thoughts of the wise are futile.”

A quote from Muhammad ibn Zakariya al-Razi - Persian philosopher (amongst other things) from the 9th century: On what ground do you deem it necessary that God should single out certain individuals [by giving them prophecy], that he should set them up above other people, that he should appoint them to be the people's guides, and make people dependent upon them?