This is oversimplifying that case quite a bit, and despite the cases findings it's been hotly disputed by economists. Putting aside that a large cornerstone of the case was that internet speeds at the time were prohibitively slow to download another web browser/application, which is no longer the case.
Large Company does something illegal, profits immensely (or else ensures a competitor doesn't profit).
Governments step in, punish Large Company with a huge fine.
Large Company still gets to reap the benefits of what it did, because the competitor is defeated, or because the indirect benefits of it's actions is worth more than the cost of the governmental fine.
Large Company lays low for a few years.
Large Company does something else illegal.
The problem is that you are assuming that monopolies are illegal, which is false. Abusing monopoly power is illegal, but there are many monopolies in the US. Local power companies are a good example.
In this case Microsoft is giving away a product that consumers want included in their operating system for free. They are not disallowing others to be installed. US Anti-trust law is designed to protect consumers from monopolies, not to protect businesses from them.
The purpose of the Act was, to quote Sherman:
"To protect the consumers by preventing arrangements designed, or which tend, to advance the cost of goods to the consumer"
The US supreme court says this on the Sherman Antitrust Act
"The purpose of the [Sherman] Act is not to protect businesses from the working of the market; it is to protect the public from the failure of the market. The law directs itself not against conduct which is competitive, even severely so, but against conduct which unfairly tends to destroy competition itself. This focus of U.S. competition law, on protection of competition rather than competitors, is not necessarily the only possible focus or purpose of competition law. For example, it has also been said that competition law in the European Union (EU) tends to protect the competitors in the marketplace, even at the expense of market efficiencies and consumers."