Tony Stark did not like to be handed things. He didn't like it when people touched him without warning, and he wasn't a big fan of hugs.
And he certainly didn't like cuddling.
And awake-Pepper understands that. She lies down on her side, and in his oversized bed that means they don't touch.
But it only takes sleeping-Pepper about two minutes to traverse the bed and be against him, snuggling.
He's tried to move her back to her side of the bed, but she's more like an octopus than woman at that point, and he usually ends up giving up with her arms completely around him and her drooling into his shirt.
This has been sitting on my computer for months because I wasn't sure I liked it or how it ended, so I'm just throwing it up here as is and hopefully I'll come back and fix it later.