No, they don't "hate" Thor, many writers probably don't get his character but I doubt a company feels hate towards one of their staple and most recognizable characters.
Need I remind you, despite how badly he's been treated by Aaron, Thor is still a massive powerhouse and the saving grace of Midgard, he alone has saved the Earth's ass in 5 events this last decade alone (Siege, Fear Itself, Infinity, Secret Empire, War of the Realms) with 3 of those being Thor centered stories that encompassed the entire company.
On the contrary, I think Marvel does see a lot of potential in Thor, but in trying to make his appeal for mass consumption, he is losing the characteristics that made him unique.