Actually, we don't know how their relationship was. We can only assume, but since Ariadne was "useful" to Cesare and he even called her innocent (alluded to be an insult there), he most likely used her to kill Alphonso in the first timeline - she was already Cesare fiancee that time, and in love with him, so she was easy to use (and it's alluded that Alphonso was in love with her later then - it's later in the comic)
It's true that Isabella told Ariadne about what "Cesare said", so it's most likely a lie, but Cesare also tells Ariadne he never loved her and doesn't care for her - so we may assume, even if he had some feelings for her - they were never strong or they were never "love" we think of.
Ariadne is smart, fast and when in love, loyal to the core - I'm sure he appreciated those in her, but not enough for him to respect her - as I think he never really did :'/

So I was curious cause of what Ariadne said in the last chapter about why would Cesare choose Isabella and so I went back and read the first 2 chapters I would encourage everyone else to do it but Cesare and Ariadne where actually okay it wasn’t until like 7-8 years after Alphonso’s death where they started having issues and that whole her ‘udders’ thing is coined from Isabella telling Ariadne that’s what Cesar said right before killing her in all it’s looking to me like the biggest villain is Isabella I’m starting to think she knew more behind the scenes and there are some scenes where we don’t even get to see cesares face and he doesn’t even answer most of ariadne’s questions prior to her getting locked up because yes he locks her up she’s alive up until cesares coronation day