Six Flags IS a theme park, even if it isn't as high a quality one as the Disney parks.
The theme, initially, was right there in the title: Six Flags. The initial park, Six Flags Over Texas, was themed around the six flags that had, at one time, flown over the state of Texas and thus had several themed sections (or lands) around the park, i.e. Spain, Mexico, Confederacy, U.S.A, France, etc. (In fact,
Disneyland essentially created the theme park and any park that has designated "lands" would also fall under the theme park moniker). As the Six Flags brand grew, obviously the theme changed as well and once Warner Bros. bought the park, the theme became Warner Bros., hence the Merry Melodies/Looney Tunes and DC comics-themed areas, rides, and walk-around characters.
There's no denying that Six Flags, and various other theme parks, pale heartily in comparison to Disney. Disney was the first and still the best when it comes to theme parks, but to deny that such parks are classified as theme parks is just ignorant. Just because a theme isn't as well-done or overt as it clearly is in Disney doesn't mean it isn't present.
It's a moot point anyway, as these days the language has evolved such that theme park and amusement park tend to be fairly interchangeable. To quibble over the terms is pure semantics and a bit of a fool's errand.