It's really an issue of public perception. The ranking of cities by looking at crime statistics is heavily skewed due to the wide variety of the nature of political boundaries (and not one of use observes these political boundaries in our daily lives). There are approximately 2.8 Million people in the St. Louis metropolitan area. Roughly 350,000 people live in the City of St. Louis.
St. Louis City is relatively a poor city. In a region of 2.8 Million residents there is going to be a substantial population living in poverty. In cities similar to St. Louis (rust belt, significant minority population, etc.) there is going to be the affects of white flight and urban blight. The crux of the issue here is that the overwhelming preponderance of this population segments and development challenges are within the small geographic area constituting the City of St. Louis.
Parallels exist in cities like Cincinnati, Cleveland, Chicago, Pittsburgh and elsewhere, but because none of these cities have a single political boundary that holds the most troubled parts of the entire metropolitan region crimes statistics are diluted. This study and others like it do not provide a usable comparison of St. Louis to other cities. That is the problem.
I don't know that this makes the report "totally bogus," assuming that what is meant is that the study is simply untrue, but it certainly is "stupid." The metropolitan area ranking of #103 of 393 isn't informative either, but it at least comes closer to comparing like-populations. The problem of course, is that no one lives in a "metropolitan area" per se, but in a town, neighborhood and street.
And in fact one organization has attempted to rank crime by neighborhood. This methodology has many problems as well, but it attempts to zero in on where people live and work specifically. In that ranking St. Louis fared much better, the "most dangerous neighborhoods" (see: Neighborhood Crime Ranking: True, Factual, Standardized Statistics Can't Lie, Can They?) included four of the top 25 in Chicago, as well as neighborhoods in Little Rock and Orlando. Other studies can make St. Louis look more progressive than it is (see: Another Study Using the City Boundary, Another Missed Opportunity to Better Understand St. Louis), which fails to offer stakeholders an accurate perspective and therefore actionable information.
"Crime" and "safety" are not synonyms, but are parallel to many people. The dissection of relative safety can only be so fine-grained, but simply including traffic fatalities and injuries to help someone better understand their chances of being injured, dying and being the victim of crime shows that living in the City is the safer choice. The greatest danger you face when leaving your home? Traffic injuries and death. But most people aren't interested in safety, but lack of crime.