The various agencies have to investigate and find a monopoly abuse. In this case Microsoft went too far to cut Netscape out of the market. One of the things they did to achieve that was the bundling.
So Microsoft used its dominant position in one market (home computers) to distort competition in another (Internet browsers). That's the definition of anti-competitive behaviour. The idea is to prevent a company that's doing well in one market from being able to obtain control of another artificially. Control over a market isn't in itself punishable but the law intends to allow natural market forces to operate.
So there's the fact that when Microsoft acted the market for home computers and the market for internet browsers were considered to be separate. People were paying for Netscape when the behaviour began so that's not entirely unreasonable, though it's a little peculiar to think about now.
There's also the fact that Microsoft used the one monopoly to obtain the other. Were history radically different such that the iPhone ended up with 100% market share then the browser policy still might not be a problem — the product was launched with the explicit feature that third-party browsers (or, at the time, any third-party apps) weren't permitted. That's still the case. So at no point would Apple have used the one monopoly to obtain the other, rather consumers would have judged that the limitation was not a troubling impediment.
As for notepad, paint, etc, they don't matter either because they've always been inherent parts of Windows and/or because they would be considered a natural part of the desktop.
Putting the legal abstractions aside: at no point was there some other company producing far and away the most popular examples of something like notepad or like paint that Microsoft brushed aside through brute force of its desktop position. Conversely there was such a browser manufacturer. Bundling was only one part of what Microsoft were found to have done but it was something the court could realistically attempt to remedy with its existing powers.
The point is to protect the markets and allow consumers to use their free will so that if there is a single dominant player then it gets there on merit. The system's imperfect but all justice systems are and the stink of the various agencies acting against Microsoft is part of what gave Firefox a push.