maybe because Appleajack doesn't have anything "fresh" to offer.
Twilight: She's the main character (this alone is a default for her to be favorite), she's always featured doing awesome stuff and more screen time during season premieres and finales. She's makes awesome looking spells. She smart and OCD, the fandom can relate to that a lot
Pinkie Pie: She can break the 4th wall, you will never know with what she'll come up with.
Fluttershy: She cute, adorable, beautiful, kind and shy. The perfect girlfriend of many bronies, she can take your D'AWWWWWWS without even trying.
Rainbow Dash: She's the most lesbian least feminine of the characters. She's the awesome one, and obviously many males would like her, because they can identify with her. I don't see what's so cool about her though.
Rarity: Actually she's the target of negative comments, because people see her as the major bitch and superficial pony ever. Though she receive negative feedback all the time, people still talk about her, so she's remembered for something.
But what about Applejack? she's the most balanced of the main6, she's not a particularly "funny" character, she's hardworker, motherly, athletic, down to earth, humble and honest. Let's face it, people likes controversy, morbidness, gossip, And the rest of the mane6 can offer that because even though the characteristics I mentioned before are VERY GOOD, people find these things to be boring, there's no juice in her, if you know what I mean.
Her breakdown, is to be a workaholic...please, being a workaholic is boring on topics to discuss, that's why she's the least popular. And it sucks because Applejack is such a great character, she's the voice of reason, and people can't appreciate that.