The article itself states it as well.
Fans tend to view the original series through lenses colored by the subsequent film series and the later TV programs, especially Star Trek: The Next Generation, where the films had a higher quality of writing and attention to character arcs. Likewise, the later TV shows were much more in line with creator Gene Roddenberry's intentions to create a smarter sort of sci-fi show that touched on moral issues and social themes every week. But the original series was quite different from these later incarnations, and was forced to forgo many of Roddenberry's preferences and ideas in favor of studio demands for an action-adventure Western in space.
We already got 10 Star Trek movies that focused more on the idealized conception of the original series. Those films featured a more mature, experienced versions of the crew, and they faced their adventures in a more mature, experienced manner. The films reflected more of Roddenberry's original hopes for what the series could have been, and helped popularize the franchise so that Star Trek: The Next Generation could flourish and fully realize Roddenberry's intentions. The previous films, in other words, all moved beyond the original series.
And I agree with that.
What I don't agree with is the notion that you somehow can't criticize the new films for exactly that reason, because "they are not supposed to be like that".