This story has some small elements you'd better understand if you read the bigger fic it was meant to follow… (Do You Love Me?)
It's one of the works posted under 'nienie': http://fanfiction.portkey.org/profile/3113
The most important detail that was met with most confusion, was the fact that they levitated while making love. That's because Harry's supposed to have special magical powers strongly linked to emotions. That power runs wild sometimes, especially when it's based on love…
So it's just the power of the emotion Harry and Hermione are feeling… the intensity of their lovemaking, that is 'lifting them up'…
It was just to show the intensity of their love for each other, manifesting itself in magic swirling around them…
As for the 'Do you love me?' conversation: for those who haven't read the whole fic, posted under nienie, it's a line that holds special meaning to Harry and Hermione: they got together like that, and they found each other again, and again, once in a very dramatic way, with those lines…
Well, that's it!