[Toespi]

GOT’s entire theme has been lineage to the throne. Daenerys last comments to Jon were telling, she wanted love. The Lannister line to the throne has ended, Cersei’s incestual unborn child is dead. Daenerys and Jon’s incestual unborn child would leave little doubt as to who would inherit the throne in the future and tie Jon and Daenerys together forever.

[Bruce Campbells Chin]

Except Jon made it very clear that he doesn't want to be "together" with Danaerys. As Varys said, Jon was raised as a Stark in Winterfell, and his views on incest were formed then. As Catelyn Stark said, Westeros views incest as an "abomination".

Danaerys doesn't think it's a big deal because she was raised as a Targaeryen right from birth, and so believes incest is no big deal. So while she doesn't have an issue marrying/having sex with her nephew, Jon very clearly considers that to be a deal-killer.