I'm guessing that...
...having the highest ratings doesn't equate to high enough ratings to make Colbert's show profitable.
Like all broadcast media, late night has seen a significant decline in viewership over the last 10-15 years. Audiences decline, resulting in advertising revenue declining, all while content production costs go up.
Having the most eyes on a show doesn't mean much if it isn't enough eyes to pay the production costs.
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