Why did the Separatists want to kill Padme?

What was the reason that Viceroy Gunray and the Separatist leaders were trying to kill Padme?

It doesn't seem to make sense. She was leading an opposition to prevent the creation of an army for the Republic, which would be great to the Separatists, because they would have no one to oppose their droid army.

Instead of supporting Padme, they are eager to kill her. Why? What's their motivation? What's their goal?

Is it just revenge for her victory in the battle for Naboo, or is it something else?