Applejack and Fluttershy have never been particularly close; in all honesty they're more like acquaintances with mutual friends than actual friends with each other.
But when Winona is injured Fluttershy is the only one who can help, and as Applejack tries to pay back the debt she feels she owes the pegasus for her kindness they both discover that there might be more to each other, and their own feelings, than they realized.