It is also a blow to the Cardiff Blues star's Lions hopes but Gatland remains open-minded.
"Rob Howley was right to stick with the same team for the Italian game, and right to name it early to defuse a week's worth of focus on Sam not being picked," Gatland told the Western Mail.
"But Sam will play many more times for Wales, and he'll captain Wales again.
"In terms of the Lions, of course he's still in contention. Nobody is ruled out.
"I would compare Sam's situation to some of the guys in Stuart Lancaster's England squad.
"If you take people like Manu Tuilagi, Dylan Hartley, Courtney Laws, they were all heavily talked about for Lions spots but have barely figured as yet in the Six Nations.
"That's the prerogative of their national coaches, whose first responsibility is to get the best out of the team and make sure each individual performs to his potential.
"But look, there's a long way to go before we select the Lions squad, we're only two matches into the Six Nations and we will also be looking at players' club form after the tournament.
"When you are picking a squad of 36 or 37 a lot of different factors come in to the equation, you have to think about combinations being right and having cover in certain positions.
"Sam isn't starting against Italy, but Rob put his faith in a winning side and I totally understand that.
"I am just grateful that there is a really healthy rivalry between Sam and Justin Tipuric, one that should be celebrated rather than them being pitched head to head all the time.
"That position is so attritional, both are going to pick up injuries along the way and so both are going to play a lot of Test matches in their careers."
Ryan Jones, a Lion in 2005, will lead Wales in Warburton's absence and he has backed his teammate to bounce back.
"Sam is the Wales captain and he is a bright kid with a bright future," said Jones.
"It has amazed me the reaction this issue has had because Sam's role within the squad does not change.
"I have a huge amount of respect for Sam as a player, bloke and captain and we have spoken about a number of things."
Warburton had been a favourite to lead the Lions in Australia but Jones, who is also a contender, reckons it is not yet a concern.
And he has pointed to his personal nightmare in 2009 as a fitting example.
Jones was the pre-tour captaincy favourite but missed out on original selection. He was called up following Wales' tour of Canada and America but was ruled out with a head injury upon his arrival in South Africa.
"Things like the Lions captaincy will take care of itself," added Jones.
"It will depend on who is going, the team make-up and what the coaches want.
"There are so many factors outside your control and it is not like applying for a job. First of all, you have to get on the tour and then you could be offered the role which is not for everyone.
"If any player tells you now they are not thinking about the Lions tour, they are lying. You have one eye on it but it's a balance.
"The thing about the Lions is we start talking about it earlier every tour. People speak about it in pubs, my dad is talking about it and that is what makes sport wonderful.
"But for players, first you have to be fit and secondly you have to be playing well. I know this more than most!
"In the end, I was not playing well enough to go on the plane. That is a fact of life."