Despite what several hundred people claim on the FM forums, the game gives no preference to human or AI managers.
At the core, Football Manager is a giant spreadsheet and has thousands of permutations calculated using it. Now, this could be something simple as an attacking player with skill of the ball at their feet against a defender with a tackling attribute but in truth, the game would also factor in things like work rate, energy levels, motivation and morale as well as many others.
Not forgetting of course, the hidden attributes that can only be viewed with the editor. These include ambition, consistency, controversy, important matches, injury proneness as well as others.
The managers input is also important in choosing a formation which could be used to man mark a specific player or go all out attack. This is where the AI will have an advantage because it will change things around and it does learn and adapt. If a human manager always plays their games in a 4-4-2 formation and always uses the wings to attack, the AI will change their tactics to counteract this. You'll also get an in game email where the "fans" start asking about always using the same formation when it isn't working.
Finally, there's the random factor which will also affect things and why, you could play the same match 10 times with the same players against the same opponents and get 10 different results.