The 25-year-old has started only seven games since joining the club from Roma in a £18million deal last summer.
The Italy international’s debut at Anfield was delayed by an ankle injury.
Benitez said: “When you have been injured for a while it’s not easy for a player. Then, when you are available and the team isn’t doing well, it makes it even more difficult. You have to decide if you can afford to give him two or three games when you know he’s maybe not at the level he could be, so you could end up losing some of them.
“Alberto isn’t stupid. He knows the priority now has to be the team and what’s best for that. All he can do is keep training and make sure he is ready when we need him. But as I said, the most important thing we have to think of is the team, not one player.”
He added: “When I didn’t play Alberto at Wolves it wasn’t to do with the state of their pitch, it was because of the kind of game and because others were available, which meant we could manage in a different way. So whether I play him at Wigan or not isn’t a decision that will be determined by the pitch.
“But we have had a conversation about things and he knows the situation. Alberto is a very good professional, who was a big name in Italy and wants to show his quality here. When you’re like that but cannot play for three or four months and then you’re available but can’t play because the team is maybe doing really well or has problems, it’s a difficult situation for any professional.”