The original Six Flags theme park was Six Flags Over Texas. The name referred to the six different countries that have governed Texas - Spain, France, Mexico, the Republic of Texas, the United States, and the Confederate States - and the park retains a theming based around the state's history. The Six Flags company has opened many more parks in other states throughout the United States, but needless to say, none of those states have ever had six flags over them- nor do the parks have any real theming.
They used to at least make an effort: The second and third parks in the chain were called Six Flags Over Georgia and Six Flags over Mid-America (now Six Flags St. Louis), and both made an effort to use a similar six-nation theming as Over Texas did, but they stretched it pretty far- St. Louis has as its "six flags" France and the United States (both of which are legit), but also Spain (which claimed the region but never actually had all that much influence there), England (ditto), Missouri (part of the US, so it's kind of cheating), and Illinois (not only cheating, but the land the park is on was never part of Illinois); and Over Georgia counts France (whose history in Georgia is negligible) and Georgia itself, which has never been a real sovereign state under its own power. The company stopped building parks after these first three in favor of buying up existing locations, and never bothered to keep up the theming convention afterward.
Epcot is an acronym for the "Experimental Prototype Community of Tomorrow", and was so named in the mid-1960s due to Walt Disney's intent to build a working city of the future in central Florida. After his death the plans fell by the wayside, and the park that eventually opened as Epcot in the early 1980s was called EPCOT Center, with Disney claiming that the theme park was the center of EPCOT (aka the "official" name for their entire Disney World property) and that a city would come eventually. They dropped this approach in the mid-1980s when Disney's upper management changed, and renamed the park as simply Epcot in the mid-1990s as part of a re-branding effort to move the park away from its "edutainment" roots.
Disney's Hollywood Studios has suffered this trope twice over. The park opened in the late 80's as "Disney/MGM Studios" and retained that name long after the Disney-MGM partnership ended (indeed, some fans had taken to referring to the park as simply "MGM"). In 2008, the park was renamed "Disney's Hollywood Studios". Nonetheless, this new name remains a victim of this trope, as the park's actual animation studio closed in 2004. Of course, the park isn't in Hollywood either, so it can be assumed that the "Studios" part is now just supposed to be a fictional element of the park experience.
The Busch Gardens parks in Williamsburg, VA and Tampa Bay, FL got their names after the Anheuser-Busch brewing company which also owned Sea World. In 2009 AB sold their entertainment corporation to the Blackstone group but the parks are still permitted to use the Busch name.
Knott's Berry Farm started off with the Knott family selling berries, pies, and berry preserves beside the farm. Eventually, a fried chicken restaurant was created, and grew so much in popularity that a ghost town and various other attractions were built to entertain guests as they waited for a table. Over time, the attractions grew so much that the Knotts began charging admission, and the attractions would eventually overtake the restaurant and farm itself. The name became fully artifactual in the 1990s when the Knott family sold it.
Kids in the Scotch Plains, NJ, area still often go to the small Bowcraft Amusement Park on Route 22 for birthday parties and general weekend fun. How did the park get that name? It was opened right after World War II as an archery supply store with a practice range. Later the owner added a ski store and small ski slope. More and more attractions followed, and like Knotts Berry Farm on the other coast the name is the only link to the property's original use.