This is a problem that made me switch to Fedora for a while but I've finally found a solution for fixing Eclipse on Ubuntu and fixing the Aptana plugin as well.

The thing is that when you install Eclipse on Ubuntu it also installs GCJ and uses GCJ by default.

So you must do it like so.

If you don't have Eclipse installed go to
System > Administration > Synaptic Package Manager

type eclipse in the quick search. Check it

Then type sun java and check sun6-java-bin and sun6-java-jre

Then click Apply to install them.