Marie and Louis XVI don't have the ideal relationship by any means. It takes them almost 10 years to have sex, and in the mean time Marie isn't exactly faithful. But the pair share a few sweet moments throughout, including flirtatious whispers and knowing glances that show their relationship blossoming.
Then at the end of the film we really see the love between them when Marie reaches over to hold Louis's hand at the dinner table before the family is forced to leave Versailles. Especially when we know Marie's doomed fate.