Charles's suspicions were based on his observations of the Foundation's actions. Although the Foundation claimed to be secretly protecting humanity, Charles hadn't seen them protect anything.
If their initial efforts to stop the Pope's plan had failed only because of the Light God's interference, that would be one thing.
But when sunlight was killing the people of Earth Sea, they still didn't lift a finger to help, merely watching as the island's inhabitants died.
When it was necessary to seek Darkness to save Earth Sea, they still had no intention of making contact with the people there, going about their own plans alone.
Although they verbally claimed to be saving Earth Sea, observing their prior actions, everything seemed quite suspicious.
Charles still remembered when he was on Dream Island 041, meeting Aaron who swore his oath to the Foundation.
"We battle in the Darkness so that humanity can live in the Light, protecting people from the threat of abnormal projects!!"
