When Microsoft packaged Internet Explorer with Windows, they were sued for antitrust violations. However, today every operating system has its own built-in browser, including ones by the companies that complained about Microsoft (Google, Apple, Mozilla Corporation). What is the legal difference between what Microsoft did and what other companies are now doing today? Why do the courts target Microsoft when Apple was and still is taking advantage of its monopoly? Why can't Microsoft receive financial compensation for the damages Apple did to Microsoft?
From Baker, Donald I. "To Indict or Not to Indict: Prosecutorial Discretion in Sherman Act Enforcement." Cornell L. Rev. 63 (1977): 405:
The Assistant Attorney General must ultimately decide whether to bring a criminal prosecution. He bases that choice in part upon articulated principles, in part upon intuition gained from experience, and ultimately upon the facts of the particular case.
The choice to prosecute Microsoft and not Google, Apple, or Mozilla for (what you claim to be) ostensibly similar activities is an exercise of prosecutorial discretion. My guess is that the Attorney General's office simply does not believe the actions of the other companies rise to the level of an antitrust violation. When they believe they do, they prosecute. (United States of America v. Apple Inc., et al., 12 Civ. 2862 (DLC)).
Microsoft settled their case. No other party is responsible for Microsoft's decision to settle, even if they were doing the same thing, and even if they are later found to be guilty for or come to a settlement agreement regarding the same thing.
The Sherman Antitrust Act was written in the 1890s. It does not deal with the packaging of web browsers. It deals with monopolies and 'trusts'. (In this context 'trusts' are contracts between companies to fix prices and create effective monopolies. This was a major problem with steel and oil in the 1890s.)
It was alleged that Microsoft conspired to restrain the trade in web browsers, and attempted to create a monopoly in the web browser market place.
The relevant text is
15 U.S. Code § 1 - Trusts, etc., in restraint of trade illegal; penalty
Every contract, combination in the form of trust or otherwise, or conspiracy, in restraint of trade or commerce among the several States, or with foreign nations, is declared to be illegal. Every person who shall make any contract or engage in any combination or conspiracy hereby declared to be illegal shall be deemed guilty of a felony, and, on conviction thereof, shall be punished by fine not exceeding $100,000,000 if a corporation, or, if any other person, $1,000,000, or by imprisonment not exceeding 10 years, or by both said punishments, in the discretion of the court.
15 U.S. Code § 2 - Monopolizing trade a felony; penalty
Every person who shall monopolize, or attempt to monopolize, or combine or conspire with any other person or persons, to monopolize any part of the trade or commerce among the several States, or with foreign nations, shall be deemed guilty of a felony, and, on conviction thereof, shall be punished by fine not exceeding $100,000,000 if a corporation, or, if any other person, $1,000,000, or by imprisonment not exceeding 10 years, or by both said punishments, in the discretion of the court.
(At the time of the Microsoft prosecutions, the fines were lower.)
The background: Microsoft were the dominant purveyor of computer operating systems at the time of the "browser wars", a time when numerous browser companies were selling internet browsers or otherwise providing them for free to the market.
Microsoft started giving away Internet Explorer as an integrated part of Windows. They were also alleged to have changed or exploited the way Windows worked to make that integration very tight, to the exclusion of competing products. (By not exposing key APIs publicly.)
The prosecution's case was that Microsoft used its market power as the dominant operating system provider in an attempt to monopolize the browser trade, which it regarded as a separate area of trade. It was argued that this was an intentional and deliberate process to exclude and kill off competitors.
Paul Maritz, a senior Microsoft vice president, [is alleged to have stated] an intention to "extinguish" and "smother" rival Netscape Communications Corporation and to "cut off Netscape's air supply" by giving away a clone of Netscape's flagship product for free.
In the first trial, the prosecution were successful, and a break up of the Microsoft Corporation into separate companies making different products was ordered as a remedy. However on appeal the DC Circuit Court of Appeals quashed the lower court's finding and held that the judge in question had not merely committed errors of law but acted unethically in other matters on the case.
Microsoft and the Department of Justice later reached a settlement.
Wikipedia has a nice description if you are interested in the soap opera side of the case: https://en.wikipedia.org/wiki/United_States_v._Microsoft_Corp.
It has been suggested in the other answer that the US Attorney General could simply decline, as a matter of prosecutorial discretion, to prosecute clear breaches of the Sherman Act committed by Microsoft competitors. However, the Sherman Act also creates a duty on US Attorneys—
it shall be the duty of the several United States attorneys, in their respective districts, under the direction of the Attorney General, to institute proceedings in equity to prevent and restrain such violations.
Now in your question you say, "today every operating system has its own built-in browser"—the background is quite different to that of the 1990s. Apple, Microsoft and Google, are competitors in many spheres. My belief is that it would be quite difficult to accuse any of them in conspiring to create a monopoly, because there are many alternative products one can use these days to achieve the same ends. Moreover, all of them have learnt from the prosecution of Microsoft that there are limits to how tightly products can be bundled.