It seems to me that there is a slight difference. It's just a subtle difference though. The first one refers to something that hasn't happened yet. For example someone says to you: "If I leave my house unlocked, you will probably steal my TV." And then you could reply: "What makes you think that I will do that?"
The second one could also refer to something that happened in the past. For example, when someone says to you: "I think you stole my TV." You could answer: "What makes you think that I would do that?"
It's very subtle, I know, and in many cases they are both applicable.