What made Vicksburg so difficult to capture?

Geography, because its well-defended cliffs could not be attacked from the West. But Grant had been distracted from his original march down the East bank of the river, by the intervention of the political general John McClernard, who had raised a private army, with secret orders from Lincoln and Halleck.

Why Grant could not be told about this directly is unclear. Perhaps Lincoln didn't want to encourage too much talk about private armies.