I prefer to be on the left in a two-man pairing, how about you?

[2feet]

Seriously though, does it actually make any difference?

I have a CB and he prefers the left (like me), but my system requires him on the right so I played a whole season with him on the right, and the game keeps telling me he's a bad fit.

But his performances seem good, so.... ???

[FrazT]

Like a lot of in-game advice, ignore it if he is performing well.

[HUNT3R]

The preference does not have any effect other than helping AI team selection.

[talhak]

I give attention to side preferences as much as possible. From my experiences, I can say that it affects the player's performances. But as @FrazT said, you may ignore this advice if he performs well.

[Feddo]

I have had many players (mainly strikers) that don't perform well on there preferred side. Simply because my tactic worked better when the where on the other side. 

[HUNT3R]

11 minutes ago, Feddo said:

I have had many players (mainly strikers) that don't perform well on there preferred side. Simply because my tactic worked better when the where on the other side. 

This is a good point to make. Footedness will also play a part in how a player performs, so it's important to take note of that as well.

[Draakon]

Consider this as his individual preference. Just like a shirt number. You could make him happy and play him where and in what role he prefers, but you could also give him other instructions on the pitch.

In reality the question of preferred position/role usually comes under discussion when contract extensions are negotiated. You have to be careful when making promises about that, but you can also take these clauses off the table and just offer money instead.