An article posted in r/history about Mormon archaeologists has this to say:
Smith's account of buried wonders was one of many in the United States at the time. As white settlers moved west, they encountered mounds filled with skeletons and artifacts, including beautiful pottery and ornaments. Newspapers, including those in Smith's hometown of Palmyra, New York, buzzed with speculation about who the "mound builders" were and how they came by their refined culture. Many settlers, blinded by racism, concluded that the mound builders—now known to be indigenous farming societies—were a lost people who had been exterminated by the violent ancestors of Native Americans. The Book of Mormon, with its saga of righteous, white Nephites and wicked, dark-skinned Lamanites, echoed these ideas.
I'd love to know what some of the other popular theories were, and how widely these beliefs were held. Did most Americans not believe that natives could have done these things? Also, the narrative of the Book of Mormon has always struck me as odd, outlandish, and hard to believe, but would this explain why so many people were taken with it?
I'm going to borrow from an earlier answer:
Archaeology was beginning to come to grips with the extant of Native American prehistory in the United States during the 1930s, but even in Henry Clyde Shetrone's The Mound-Builders (1930), the author felt the need to emphasize that all these mounds were created by Native American peoples, and not some "Mound Builders" that were not Native American had built these and then died out - a very popular idea even well into the 1930s in the pulps. To prove his point early on, Shetrone quotes J. W. Powell:
For more than a century the ghosts of a vanished nation ... ambuscaded in the vast solitude of the continent, and the forest-covered mounds [were] usually regarded as the mysterious sepulchres of its kings and nobles. It was an alluring conjecture that a powerful people, superior to the Indians, once occupied the valley of the Ohio and the Appalachian ranges, their empire stretching form the Hudson Bay to the Gulf, with its flanks on the western prairies and teh eastern ocean; a people with a confederate government, a chief ruler, a great central capitol, a highly developed religion, with homes and husbandry, and advanced textile, fictile and ductile arts; with a language, perhaps with letters--all swept away by an invasion of copper-hued Huns from some unknown region of the earth, prior to the landing of Columbus.
The "conjecture" that Shetrone alluded to was that there was a precursor people to the Native Americans, who had a relatively high degree of culture and civilization that was destroyed when that hypothetical people were overcome by the ancestors of the Native Americans and destroyed. It's sort of the inverse of the "Noble Savage" idea, since it's essentially a racialist notion that denies Native Americans themselves could create what white people saw as civilization. One popular example of this kind of idea is in the Book of Mormon, which talks about the Nephites, Lamanites and other groups that settled the Americas before the Native Americans. In literature, these precursor groups were often called "The Mound-Builders."
It was fairly common belief even in the 1920s and into the 1930s; Shetrone's book has a number of additional examples from early American literature, but to give an example from my own reading, Robert E. Howard expressed the essence of this idea in a letter to H. P. Lovecraft from October 1930:
And that stuff they pull about “everybody being foreigners except the Indians,” makes me fighting mad. Then the Indian is a foreigner too, because he was preceded by the Mound-builders. And the Gaelic-Irishman is a foreigner because the Picts came into Ireland before him. And the Anglo-Saxon is a foreigner in England because the Cymric Celts were there when he came.
You might contrast this to the introduction to the young adult novel Mog, The Mound-Builder (1931):
The Mound Builders of the central west are, so far as we know, the earliest Americans. Their strange burial and effigy mounds scattered throughout the Ohio and Mississippi valleys contain the earliest records of the human race on this continent so far disclosed by archaeological research, and I have tried, with the excellent data available, to picture the adventures of a boy who might have lived at the time these interesting relics of an earlier race were being built.
The skeletal remains of a hunter buried with the skulls of three wolves in his grave with him, recently found at Fort Ancient, Ohio, along with the discovery of the fact that there were two different groups of people dwelling there at about the same time, suggested the story of Mog. I prefer, however, to believe that the Long Heads, who were the smaller of the two groups, were not held in slavery by the Mound Builders as has been thought probable by archaeologists, and I have tried to suggest a way they might have become associated with the stronger race of Mound Builders. I am grateful to Mr. H.C. Shetrone, Director of the Ohio State Archaeological and Historical Society for the information contained in his excellent book, "The Mound Builders," and to Mr. Alfred D. Moore, of the Church School Publications for his many suggestions. I am also indebted to the unsigned authors of the many pamphlets about the various mounds now preserved as historical relics in Ohio.
"Long heads" refers to cephalic index studies, where "long-headed" (dolichocephalic) was mistakenly used by many folks to indicate northern Europeans, and higher intelligence in general. These racialist concepts were being challenged and overcome by Franz Boas and others in the 1910s-1930s, but once the public takes an idea they can be hard to root out.
Shetrone claimed that the idea of a separate race of "Mound Builders" was already prevalent in 1797 when Dr. Benjamin S. Barton published New Views on the Origin of the Tribes of America (Shetrone 14), but pre-1800s Americana is a ways out of my bailiwick.
There's quite an extensive literature on the Book of Mormon and the influence/interpretation of the Mound Builders out there, but I hope that gives at least some indication of the prevalence and nature of the beliefs regarding the Mound Builders even as relatively late as the 20th century.