What drives a poor reputation for the Rogue class?

[LudicSavant]

These abilities don't allow you to use the Disguise Kit and/or make Charisma(Deception) rolls, they make you so good at them that, in the vast majority of the time, you get to bypass those rolls

This is my interpretation as well. It doesn't make the action possible, it makes it so you don't need to roll.

The question is how big a deal this is, and how it compares to what alternative builds have to offer.

A non-Assassin wants to make a disguise? They roll, using their Disguise Kit proficiency (assuming they have it; otherwise just a flat Attribute roll), and set the DC of their disguise, which is used going forward until they either succeed at their objective or until their disguise fails. Even so, it's possible your disguise is flawless but fails through different scrutiny; you didn't forge a background, establish relations, etc. You may "look the part" but fail to "check out" when investigated.

There are checks for forgery and the like too. It's the same thing as disguise; the assassin makes it so you don't need to roll those checks.

It makes you immune to Passive Investigation/Perception checks; you never have to worry about them.

This, however, it does not necessarily do. Per the PHB, passive checks are used when the DM might not want to reveal the result of the roll, or they want to represent the result of a task done repeatedly. It's called passive because the player doesn't roll, it doesn't mean that the character is being casual or passive.