It's not entirely accurate to say they were all gay, but homosexuality was certainly present during Western Expansion. Your professor was most likely just poking fun at how modern pop culture depicts cowboys as tough, masculine, ultra-heterosexual symbols, but in reality, the "cowboy" sub-culture was much more diverse. In pre-1900s literature, the cowboy was defined as an undesirable, dirty rapscallion, but he was somewhat forgiven by readers because he was an American renegade trying to survive on the frontier. These men were certainly tough, but not everyone was opting to save the damsel tied to the train tracks, if you catch my drift.

Historian Clifford Westermeier discovered an old cowboy limerick that goes like this:

"Young cowboys had a great fear

That old studs once filled with beer

Completely addle’

They’d throw on the saddle

And ride them on the rear."

Sir William Drummond Stewart is known for his queer escapades in the Western frontier and William Benemann points this out in his book Men in Eden: William Drummond Stewart and Same-Sex Desire in the Rocky Mountain Fur Trade. Stewart actually ends up bringing his boyfriend/lover back with him to Scottland and refers to him as his bag handler or valet to keep their true relationship unknown, but they would go on to travel the world together.

University of Colorado at Boulder History Department Chairman Peter Boag wrote a book in 2003 titled Same Sex Affairs which discusses homosexuality during the twentieth century. In an interview, Boag explains that many Western communities were all-male and as a result of this, gender roles became very fluid. Boag goes on to say, “In all-men societies, it was not unusual for same sex relationships, and it was just an acceptable thing to do. People engaged in same sex activities weren’t seen as homosexuals.”

D. Michael Quinn discusses in his book Same-Sex Dynamics Among Nineteenth Century Americans: A Mormon Example, that as a whole, Americans in the 1800s could express their friendships in a very intimate way. Sharing a bed, and what we would call homoerotic behavior, was a social norm of the time. However, Quinn states that this would certainly make it easier for those who were gay to pursue relations with one of their companions. It has been observed by writers of the time, such as Owen Wister, that cowboys tended to have very intimate relationships. Historian C. Packard outlines this in his book Queer Cowboys: And Other Erotic Male Friendships in Nineteenth-Century American Literature by focusing on Wister's relationship with cowboys.

Wester traveled to the frontier to study cowboy culture and would go on to write the novel The Virginian. In this novel, our protagonist "the Virginian" is described by the narrator as a handsome horseman with tiger-like muscles. Packard points out that this character is based off someone Wester spent a lot of time with during his travels. The Virginian is followed by the narrator of the book, and at one point they spend an intimate night camping while the Virginian "spouts Pan's Philosophy" in the nude. There is nothing explicitly sexual that is referenced during this scene, but the Virginian marries a woman, Molly, later on in the book. He brings Molly to an island on the eastern slopes of the Tetons for their honeymoon, and it is revealed that it is the same location where he brought the narrator, except the Virginian brought him deeper into the forest, "in a territory more rugged and remote." The Virginian brings two separate tents for himself and his wife, he does not want her to see him naked, and it is noted that he relinquished his "adherence to an impulse-driven body."

Packard sees this novel as an allusion to the "new man" that the frontier has formed. The rustic frontier has created Herculean men that express their unsullied manhood in immoral ways. Wester also seems to note the attractiveness and physicality of his companions during his time in the West. He writes that cowboys hold a certain liberation that cannot be found on the East Coast. Obviously, Packard cannot prove that Wester had homosexual relations during his time out West, but it seems to be suggested when his notes and literature are analyzed side by side.

Like most queer history, it is hard to have an in-depth view of everything that was occurring, but there is some evidence to suggest homosexuality was definitely present in cowboy culture. One thing that is important to remember is that the frontier was overwhelmingly male so as Peter Boag suggested, same-sex relations were more tolerated in these male dominate communities and it did not carry the same connotations as it does today. I guess you could say that it was a well-known secret, but you wouldn't find two cowboys kissing at the saloon.

Obviously, Rockstar doesn't allude to homosexuality in the West, but in the first Red Dead Redemption you'll notice that John Marston will talk down to characters that make racist statements. This might have been added to the game because they wanted their protagonist to be more relatable to a twenty-first century audience, but racial discrimination between white and black cowboys was less prominent compared to East coast communities. Nat Love, a black cowboy, does not mention racial issues and discrimination in his autobiography. Perhaps cowboys were more open-minded than they are commonly portrayed as.