(SPOILERS) Questions left unanswered at the end of the train

[Kor]

I think Conan cares a lot about protecting Haibara, but he also resent Haibara withholding vital information regarding the BO(both from her memory and the floppy she claimed to have lost at Haido City Hotel). Haibara probably withheld these information probably to protect Conan from pursuing BO too agressively and killing himself in the process and resent Conan for not telling her about the BO threats because he thinks "she is not as tough as she looks(this was said during the Hattori Jodie case)". So the "the less you know the safer you are" feeling is shared by ConAi and you can't really just single out Conan for it, eventually they will trust each other more but that could be 300+ files away.

Haibara doesn't tell Conan stuff because she doesn't want him to know too much and put him at risk.
Conan doesn't tell his plans to Haibara while his plans involve putting Haibara at risk.

Haibara not telling is definitely not the same thing as Conan not telling.

Plus, Haibara's character is basically "built" around the whole nature of being secretive and distrustful (she grew up in an evil organization). It makes sense for her to not tell all of what she knows. For Conan, however, the only excuse is that he simply puts his plans before other people's feelings.

[ShinRan4ver]

I think Conan cares a lot about protecting Haibara, but he also resent Haibara withholding vital information regarding the BO(both from her memory and the floppy she claimed to have lost at Haido City Hotel). Haibara probably withheld these information probably to protect Conan from pursuing BO too agressively and killing himself in the process and resent Conan for not telling her about the BO threats because he thinks "she is not as tough as she looks(this was said during the Hattori Jodie case)". So the "the less you know the safer you are" feeling is shared by ConAi and you can't really just single out Conan for it, eventually they will trust each other more but that could be 300+ files away.

Haibara doesn't tell Conan stuff because she doesn't want him to know too much and put him at risk.
Conan doesn't tell his plans to Haibara while his plans involve putting Haibara at risk.

Haibara not telling is definitely not the same thing as Conan not telling.

Plus, Haibara's character is basically "built" around the whole nature of being secretive and distrustful (she grew up in an evil organization). It makes sense for her to not tell all of what she knows. For Conan, however, the only excuse is that he simply puts his plans before other people's feelings.

Haibara's thought process is built around running away from the BO, Conan's is built around engaging and eventually taking down the BO, ofc Conan's will be viewed as more risky and putting Haibara at risk. But without Conan's aggression the plot will never go forward, without taking risks the BO could never be taken down and Haibara would always be running away, as Conan said in episode 345: "sorry Haibara, If we keep acting like this we will never take the next step".

You mentioned Haibara's character being built around secretive and distrustful, Conan 's character is built around aggression, self-confidence and risk-taking while protecting others by keeping secrets(Ran) so you can't give Haibara a character out and not give the same treatment to Conan.

[Kor]

Yes, Conan takes risks, but putting other people at risks (specifically Haibara) for his plans is a horrible character trait, which is why I "single out Conan for it".

But Conan's aggression has nothing to do with the plot going forward, at least in the current arc. It's not like Conan was like "gotta search for Bourbon!" or anything like that. He didn't do much to advance the plot here. The only reason the plot went anywhere was because Bourbon appeared on his own accords and because the DB sent the video featuring Shiho to the Detective Agency.

And even if Conan is a risk-taker, that doesn't excuse Conan from not caring about other people's feelings or making up plans that putting other people at risk without their knowledge.
Haibara and Conan are different and they serve different roles. Haibara is a minor character and can get away with some questionable things, but Conan is out hero protagonist.

I also don't believe "Conan's aggression is advancing the plot" is a good argument since that's a bit of a meta thinking.

[El Huesudo II]

Conan is crazy. We already know he's supposed to be the Silver Bullet (especially with Akai on his team), but he's too reckless and ballsy - he's shown that on every case he takes, and it shows much more in BO-related cases. To him, Haibara is an "obstacle" - letting her in on the plan means enduring a lecture on why he shouldn't even think of doing that, and in Conan's eyes, that leads to nowhere.

Haibara is terrified, and with good reason. She is well aware of what happens to those who mess with them, and that they don't care how many people die for that purpose. To her, Conan is an idiot that can't seem to understand that he's dead, and who seems to love being on the spotlight, which he'd have to avoid if he cares about his safety and the safety of those around him.

So it's natural that they keep secrets from each other. Conan may know what the BO is capable of, but he doesn't care - hell, he seems to be well aware that his is a suicide mission and he seems to like the idea. (How Japanese of him.) Haibara, on the other hand, knows what Conan would do if she shared everything she knows about the BO, which is a helluva lot (she's a codename holder, for crying out loud); and she also knows what would happen if he makes a move.

The thing is - how much more can their friendship last if they keep being like this? The friction is only building up more every time. This is why I don't understand the people who pair them up - they simply can't have a steady, healthy relationship even if they tried; because there's no trust. Trust is EVERYTHING in a relationship. And if Conan is even considering the idea of his relationship with Ran going down the drain because how much the trust between them is damaged, he wouldn't even dream of hooking up with Haibara even if he liked her - the same rule applies.