Even as small as the income penalty is, it's not something you can afford while playing a faction that cannot handle income loss, like Germania. However, most rebels are lower-grade units, often peasants (though a handful of hestati and family members pop up occasionally), and this means that a general with a handful of units can easily clean up the threat before it starts. I see rebel armies as a chance to gain a Man of the Hour (very important for garrison duties or when I'm low on generals).