In my experience, my main seemed free from rebellion. They can happen anywhere else. I would also guess there is some chance that each state corp can be targeted each month. This means that countries with more state corps are more likely to experience rebellions. This also means that a country can experience more than one attack per month.
I recently hit 11 countries and experienced rebellions in 5 countries, 1 of them being my main. Completely shuts down 1 corporation per country, but didn't seem to be a big deal. If I continue expanding will they get worse, as in more than 1 corporation per country?