Dr. Vegapunk is the central figure of One Piece's Egghead Arc. As of Chapter 1066, "The Will of Ohara," all of the Straw Hat Pirates and Jewelry Bonney have received a formal introduction from this scientist. However, they haven't had quite the same experiences with him.
The experiences everyone has had with Vegapunk have ranged from harmless and friendly to cruel and hostile. Luffy might call Vegapunk a nice guy based on his experiences with him, but the rest of his friends might beg to differ. Depending on how they all feel about this, it could create a divide as to how to approach this man going forward.
What Experiences Have People Had With Vegapunk?
So far, Luffy has only had two major encounters with Vegapunk and his Satellites. His first encounter was with Vegapunk Atlas. She may have knocked the Straw Hat captain senseless, but it was only because he threw a punch at her thinking she was a hologram. After this, she acted relatively friendly toward Luffy and his friends. The two ended up leaving off on good terms.
Luffy's second encounter was with Vegapunk's original body, the Stella. This time, the doctor came off as a harmless klutz. The atmosphere of this scene was one of fun adventure for the group save perhaps for Bonney. In any case, Luffy has no reason to perceive Vegapunk as a threat.
The other Straw Hat Pirates' overall experience with Vegapunk is more debatable in terms of positivity. When they first met Vegapunk Lillith, she had taken the Thousand Sunny hostage with the Vegaforce-01 and even surrounded it with weaponized Sea Beasts. It was only because Zoro and Robin could have taken her down instantly that she backed down.
Later, on Egghead, they were attacked by a Jimbei Seraph sent by Vegapunk Edison. Again, the Satellite only let up because the Straw Hats turned out to be more than they could handle. There's no telling how far Edison would have taken things if the crew was any less capable than they were.
The Straw Hats finally got a positive encounter out of Vegapunk Shaka, the embodiment of Vegapunk's good side. He gave them some useful information about the ancient past and even made Robin cry tears of happiness talking about Ohara. However, he's still the one exception that this group has encountered so far. This is to say nothing of how Zoro and Brook stayed on the Sunny, so they don't even have Shaka as a point of reference yet.
Perhaps the most averse to Vegapunk is Bonney. This man is the one who turned her father Bartholomew Kuma into a mindless cyborg. With both Atlas and the Stella, she reacted angrily at the realization that they were Vegapunk. The whole reason she ventured to Egghead in the first place was to give Vegapunk a piece of her mind, perhaps violently.
Franky also has his own positive stake in this. He's interested in Vegapunk's inventions and scientific knowledge. Because of this, even after being attacked, he insists on being friends with him.
How Will These Experiences Shape Everyone's Perception of Vegapunk?
These differences in experiences with Vegapunk could create a small schism between these characters. Naturally, Bonney will want to rough up the doctor no matter what. Luffy might try to defend him as he seems okay in his book. Franky might also have a bias in favor of Vegapunk since he's interesteded in his science. The rest of the Straw Hats will have to come in on this conversation to share their own experiences. Vegapunk can be a nice guy, but he can also display inhuman cruelty in the name of science.
These three groups will have to have a serious debate over whether Vegapunk is an enemy, or at least whether he can be trusted. The other Straw Hats' experiences with the doctor and his Satellites are all over the place. Only Bonney has had enough experience with the doctor to know what he's truly capable of, and it can get pretty bad. For now, the best course of action might be to tread with caution around this man.