The meme is laughable at best. It attempts to take well rounded characters as Applejack and turn them into flat characters for a political or religious purpose. In the case of Applejack it attempts to depict her as an Atheist who looks skeptically at any sign of religion while ignoring not only the context of the episode Leap of Faith but also her character in the episodes Castlemania and another where Twilight Sparkle doubts Pinkie Pie’s abilities.
To start off a flat character is generally a minor character in a novel, poem, movie or TV show and always shows little or no change in personality according to personal experiences and. This is not the case for Applejack, who shows that she does believe in the supernatural but is not quick to believe in just any story.
To be technical, Leap of Faith is about con-artists who promise a product that apparently does not work; these con-artists are the Flim Flam Brothers who go from town to town selling products. Granny Smith seriously believes the product will make her younger and at first it seems like it actually works, but it is later revealed that belief in the product actually working helped Granny Smith gain confidence, much as how many medications allegedly work. We do live in a world where many businesses lie or exaggerate how well their products work; no reason the creators of MLP would want to teach a younger audience to be diligent about who they believe. I can understand televangelists have a notoriety of dishonesty about miracles they allegedly perform such as in the case of Benny Hinn and you can read articles on that. However, superstition should be differentiated from faith. The Catholic Church reprimands superstition as a violation of the first commandment . Sometimes excesses can be made with valid forms of popular piety and sacramental .
The allegation Applejack is an Atheist from Leap of Faith does not fit the context of her character in Castlemania in which she speaks to Rainbow Dash about the Pony of Shadows, showing considerable fear at the thought thereof. It is Rainbow Dash as opposed to Applejack who says she does not believe in ghosts, though their trials in the abandoned castle install fear even in Rainbow Dash. Does any Atheist believe in ghosts? Not that I know of. Here we see a clear belief in the supernatural on the part of Applejack. It remains unclear if she still believes in ghosts after these events.
In another episode, Twilight Sparkle aggressively searches for answers to Pinkie Pie’s unanswered and supernatural abilities. Everypony in town tells Twilight they just accept it, even Applejack who puts it the most bluntly. In the end, Twilight learns a valuable lesson: you cannot prove everything scientifically. Princess Celestia helps her to learn this. Science comes from the Latin term scientia meaning knowledge as in our own knowledge of how things occur. As we know or should know, our own knowledge is limited by our own human capabilities. That’s not to say you can’t rationally prove the existence of something. Many throughout the ages have given very detailed defenses of the existence of God such as Saint Thomas Aquinas whose works continue to be ignored by Atheists and they have not been disproven either. I might write something later on this.
 Catechism of the Catholic Church, no. 2138
 Ibid., 2111