Has this changed so much since 3E?
In the 3E DMG, p148, it suggests that the DM might consider allowing a PC to control the cohort as a secondary character, to alleviate some of the DM's load, if the cohort is well-treated and loyal. It warns that not all players can handle running two characters, though.
The strong implication is that having cohorts under player control is the exception, not the rule; generally, a cohort will do what his master tells him to, but he's still an NPC with his own personality - he's not Dominated.
What does the 3.5 DMG say?
-Hyp.