Most people are focusing solely on the bundling of IE, while the EC has actually considered another important part of Opera's complaint, namely Microsoft undermining standards:
In addition, the Commission is concerned that the ubiquity of Internet Explorer creates artificial incentives for content providers and software developers to design websites or software primarily for Internet Explorer which ultimately risks undermining competition and innovation in the provision of services to consumers.
Remember, Opera forced Microsoft to default to standards mode in IE8, so it is too bad that most people seem to ignore the standards aspect.
Then again, perhaps forcing Microsoft to adhere to standards is less controversial than unbundling IE?
What people need to keep in mind is that Microsoft has abused its monopoly, and as a monopolist one has to follow certain rules that other companies don't have to follow. Microsoft did not follow those rules, and by not doing so, they broke the law.
Opera Software did not sue Microsoft. Opera Software reported to the EC that Microsoft seemed to be breaking the law, and the EC agreed.
Breaking the law has consequences whether you agree with the law or not.