Is it normal to have a Macbook heat up when using a dual boot linux?
No, I don't think it's "normal". But as always, it depends. For me, this usually happens when I look at full screen flash video or am doing other computing intensive stuff. When I dualboot into my dev environment, I'm just surfing the web for informations which wouldn't lead to the heat up.

TL;DR: It's very likely that it's your behaviour that changes with the platform you boot into and that it's this causing the heatup.