Xjyuk

We see in Harry Potter and the Goblet of Fire that Hermione seems more that disgruntled when Fleur kisses Ron on both cheeks: (my emphasis)

Fleur bent down, kissed Harry twice on each cheek (he felt his face burn and wouldn’t have been surprised if steam was coming out of his ears again), then said to Ron, “And you too-you ‘elped”

“Yeah,” said Ron, looking extremely hopeful, “yeah, a bit -”

Fleur swooped down on him too and kissed him. Hermione looked simply furious, but just then, Ludo Bagman’s magically magnified voice boomed out beside them, making them all jump, and causing the crowd in the stands to go very quiet.

We also see that in Harry Potter and the Half-Blood Prince that Hermione was going to ask Ron to the Christmas dance/ball with Slughorn and that he genuinely seemed to want to go with her:

“‘Slug Club,’”repeated Ron with a sneer worthy of Malfoy. “It’s pathetic. Well, I hope you enjoy your party. Why don’t you try hooking up with McLaggen, then Slughorn can make you King and Queen Slug —”

“We’re allowed to bring guests,” said Hermione, who for some reason had turned a bright, boiling scarlet, “and I was going to ask you to come, but if you think it’s that stupid then I won’t bother!”

Harry suddenly wished the pod had flown a little farther, so that he need not have been sitting here with the pair of them. Unnoticed by either, he seized the bowl that contained the pod and began to try and open it by the noisiest and most energetic means he could think of; unfortunately, he could still hear every word of their conversation.

“You were going to ask me?” asked Ron, in a completely different voice.

“Yes,” said Hermione angrily. “But obviously if you’d rather I hooked up with McLaggen...”

There was a pause while Harry continued to pound the resilient pod with a trowel.

“No, I wouldn’t,” said Ron, in a very quiet voice.

Were there other reasons for this happening other than Hermione and Ron were smitten with each other or had J.K. Rowling gotten the love train started by then? If she hadn't, when did she decide to make them a couple?

A note on the answers: I do not want an answer coming from the books or movies! A Rowling interview is the sort of material that would work (Pottermore is also good).

It seems like it was planned from the very beginning. In a February 2014 interview with Emma Watson for the magazine Wonderland Rowling stated:

I wrote the Hermione/Ron relationship as a form of wish fulfillment. That's how it was conceived, really. For reasons that have very little to do with literature and far more to do with me clinging to the plot as I first imagined it, Hermione ended up with Ron.

As you can see, she claims that the relationship sprung from "the plot as [she] first imagined it", which indicates to me that it was always the plan, though the way that the books changed as she wrote them made it less natural than it might otherwise have been.