The thing is more about counter-monopoly legislation than about "morals" or whatever.

As Microsoft does have a quasi Monopoly (not matter for what reason they reached it),
the state has to enforce trust laws.
Monopolies can simply take higher prices than a "working" market. (monopolistic rent)
This is why the state has to enforce either a price on the monopolies revenues,
or implement anti-trust limitations.

Since Microsoft violated these anti-trust limitations they have to pay that fine.

The reason for Microsoft might be "un-competative" behavior, or simply that they
made the best running OS for the mass market. I does not really matter.
Monopoly is monopoly.
If Linux where the only OS on the market, beeing fully controlled by "Linus Industries", they would
be treated the same way.