Eclipse was created by IBM. In the ranks of old-line corporations, those three letters carry a lot of weight. I've been told that back in the 1960's, a common term for what's now know as the IT department was "IBM Department". Before there was Microsoft, IBM was basically Alpha and Omega for what they called "Data Processing". PHB's relied on their IBM rep to take care of tedious chores like thinking. When they had a problem, IBM told them what to do.
IBM open-sourced the Eclipse IDE back around 2001. It was a major-league IDE even then, and now it was free, which wasn't the case for most of the competition.
Eclipse is also more than just a Java IDE. Unlike most of its competitors, Eclipse is a general-purpose framework, and not even specifically an IDE - although the various Java IDE versions of it are the most popular. It's also capable of serving as an application framework, and as development platform for non-Java languages such as C/C++, Python, Perl, and shell scripting. I've used Eclipse plugins for all of these at one time or other. None of the preceding is a primary reason why companies pick Eclipse, but it is something that intelligent decision makers take into consideration.
NetBeans has a somewhat different history. Although it's a good product, it has been through a number of major evolutionary stages and name changes. Its major advantages are that since it was a production from the very people who invented Java (Sun), it should in theory anticipate improvements to Java and support Java-specific features. To a certain degree, it does, although Sun could have done more, especially when it came to JavaBean development and
JSF WSYWIG design, which are 2 aspects where NetBeans does have an edge on Eclipse to begin with. Because NetBeans doesn't attempt to be all things to all people, it does tend to provide better support for "grunt" development, whereas Eclipse is more my cup of tea, since I'm more prone to develop systems with multiple components interacting in complex ways and non-Java components.
None of the major IDEs is really all that bad, and each has its own particular set of virtues. To a certain degree, it's just a matter of figuring out which horse you want to place your bet on. As the saying goes, "Nothing succeeds like success", and Eclipse has been successful for a very long time now.