I don't know where to begin, really. The guy you linked is a crackpot pseudoscientist, not at all representative of a 'prehistorian'. The guy is not an archaeologist. Your comparison is a bit like asking whether archaeologists have a bad opinion about historians because you saw an interview with Mahmoud Ahmadinejad or David Irving.

We have a number of flaired users (those of us with black flair, really) who are specialised in prehistory. I regard prehistory (and the archaeological method) as one group of tools that we use to learn about the past, where history is another.

The "lost history" crowd has had a bad time of it over the last century.

Genetic studies are giving us increasingly accurate maps of the history of human migration. Combined with the tools of archaeology and linguistics, we're reconstructing prehistory in ways that were unimaginable a few generations ago.

We can see that there are no genetic traces of domestication in common animals or crops before the conventional timelines. We see no signs of industrialization or anthropogenic impact (from industry or agriculture) in ice core samples or tree rings.

Could we find more sites like Gobekli Tepe? Absolutely. But they're not going to lead to upheavals like those Randall Carlson or Graham Hancock desperately wish for. There is no deep, hidden prehistory whose traces remain in artifacts all around us - except the one patiently built, brick by brick, by the experts Carlson is rejecting.

The thing with prehistory is that a lot of the details are lost to us. There is no written record to draw from for the culture in question. What we have at our disposal are comparisons to other recorded cultures that may exhibit similar practices in some but not always all aspects. This requires us to shore up our arguments with a lot of facts and a lot of work because it is a guess, but at least it can be an educated guess. You look for patterns in the material culture, you look at the small details at what is left over, you look at nearby societies and cultures and what they were doing, and you make a guess.

For my area we have a wholly unique architectural structure that has no analogy elsewhere in Mesoamerica. There is nothing we can compare it to in order to better understand it. So instead we look at what is left and what is available. We have ceramic dioramas, we have ceramic vessels, we have ceramic figures, and we have the remains of their buildings. Well, the ceramic vessels only contain geometric or abstract shapes and there are no vessels that depict people, animals, or other common symbols used elsewhere in Mesoamerica. So we can't draw pictorial information from them, but we can draw distribution information within a site and within a region to see where these were coming from, where they were going, and how they were being used. The dioramas depict simplified versions of the architecture showing activity including a pole in the center of the structure with a person balanced on top. The figurines have some characteristics that may be considered high status, but the large amount of them do not. So there is no representation of rulers or kings. The buildings are circular, symmetrical, and no one platform on the structure is more ostentatious than the other. This has lead some to believe that this society was a corporate society in which multiple groups competed with one another for power and ruled together. They conducted a pole ceremony with all groups participating that strengthened their culture and identity. Comparisons have been made elsewhere within Mesoamerica like Teotihuacan which is a much larger city with more material culture to draw from including scenes on vessels and murals. Yet Teotihuacan, like my area, doesn't exhibit the characteristics of a central ruler like the later Aztec whom Cortes and his men encountered.

It's a guess, but a reasonable and educated guess that can change in light of new information. That guess has changed if one looks through the literature at places like Teotihuacan or within my own area.

I think that's what makes history such a fascinating subject. Archaeology is like solving a puzzle and the artifacts are the pieces to that puzzle. Some just come in more pieces than others :)