At the end of Avengers: Endgame Iron Man
snapped his fingers with the Infinity Stones to erase all of the villains.
As Tony does not know
who Gamora is.
How can she survive this as she was coming with Thanos and was considered as a bad girl in the beginning of the battle?
Last we see of Gamora is during the battle where she has a little spat with Quill, after that we don't see her. For all we know she does actually survive the battle and Tony's snap.
Gamora was seen fighting for the good guys on the field in the battle and Tony at least knows her name because Quill mentioned her multiple times in front of him. It stands to reason that in the off screen time on Titan in Avengers: Infinity War he may have described her more to see if they had seen her. As such he may have excluded her.
And if the previous point doesn't float your boat Tony might not have seen her in the battle anyway and as such might have excluded her on the grounds of not knowing she was there to be snapped.
As Paul D. Waite mentions in a comment Tony may have just decided to wipe out Thanos' forces and the Stones/Gauntlet themselves may have decided what constitutes someone working for Thanos. As Gamora had switched sides at this point it may have left her alone.
What's Tony got to do with anything?
Neither did Thanos know half the people in the Universe. In both Infinity War and Endgame it's implied that the stones are displaying some level of sentience in carrying out complex implementations of simple directives ("Kill half of everybody," "Kill all the bad guys") and that their awareness of the current state of reality includes who's naughty and who's nice - and, as such, would be aware that Gamora switched sides 7 scenes ago.
The Snapper decides who lived and who dusts out of existence as mentioned in the answer here.
Tony couldn't risk killing innocent people in the process. So, this is what his actions could have actually meant: "Anyone who's allegiance is towards Thanos should be dusted".
Since the past Gamora changed her sides and joined the present-day Nebula, her allegiance towards Thanos ended. This could be the reason why she survived the snap (considering she did survive the snap).
And it's left to the stones (maybe the Soul Stone or Mind Stone) to identify if she really parted ways from Thanos.
Tony Stark spent a lot of time with Nebula. She might have told him about Gamora. So he definitely knew about her.
Gamora was never with Thanos, she was always setting herself up as a control rod to kill him if he ever got close to reaching his ultimate goal. Since she would remain close enough to kill him if she pretended to be loyal she did not have another, better choice to stopping him. Consider her origin the Mad Titan wiped out her mother and half her world then took her. She was playing a very long game to get her personal justice and along the way she was being made stronger and understanding more about his ultimate goal and trying to find a way that she would stop him, she herself. During her personal journey she had to keep closest to him and within his innermost circle of trust which meant completing with Nebula with Zero chance of compassion, as that could jeopardize her mission. Consider meeting up with the Guardian's and taking one or more of the stones out of play the first real chance she had to break out of a lifetime undercover as an evil 'daughter' and show her true self. I'm just amazed Thanos did not realize this at some point, at least enough to know how deep down he failed and thus disqualify the love he thought he had for her, and then regain that love with the respect she maintained for her true purpose - to Kill Thanos/Stop his Infinity Stones quest. I think there was a missed repartee just before he sacrificed her for the soulstone. She could tell him how she really felt, he would get angryish and sad she could then say this disqualified her as a sacrifice, then he would make peace with what he made her and respect her will and love her for it , maybe even more.
