I suspect you're using it as a glorified text editor instead of an IDE

Your suspicions are unfounded, I have never had an issue with Netbeans builds or it rewriting my files. It is a pluggable build systems where the build.xml is a templated file that pulls in the files that you are supposed to edit such as build-imp.xml and project.properties. These files do not get overwritten. I suspect you are using the build system wrong.

Further I like that Ant is used for the build because it gives me a head start on something I would end up having to write anyways. The build file is generated when you create a project, it saves a lot of time and is standardized. As for the org-netbeans-modules-java-j2seproject-copylibstask.jar it is a jar, I don't find it to be a big deal to install it on the build machine given the amount of time saves having the default build and deploy script generated for me.

The build script gives you a starting point not and end solution for testing, custom build instruction and other build related stuff you have to put in your own files and plug them into the build not edit the build directly. I don't find it that difficult and I think it is offset by what netbeans does for you. Further, on the remote occasion that Netbeans wants to rebuild the build.xml file it always prompts you before it does so, but even with that, you should not be modifying the build.xml you should be creating your own build files and importing them into the build system. Netbeans does this so when you add stuff like web services, JAX-B generated classes, JPA change from Glassfish to WebSphere it can auto generate all of the build and deployment instruction for those items. For me having all of that boilerplate stuff generated is a huge time saver for only having to make the trade off of keeping my custom Ant instruction in a separate file and copying a jar to the build server.

As for Hudson I cannot comment, we use Cruise Control,

It is not very organized. If you go into the "Options", it has 5 big buttons at the top. Most things are in the "Miscellaneous" section.

Not a show stopper for me, I spend all of 45 minutes in there when I do a fresh install and then I never touch it again. It does not affect my day to day work. This is also a preference thing not an issue with how Netbeans performs as a development environment.

The debugger and profiler are really slow.

I have never had an issue with the debugger being slow on my machine. I will give you that my Machine is top of the line so it may not be exemplary of the standard, but still no issue. In fact Netbeans has a feature that I have not seen in any other IDE, that is a must have for me now. And that is the fact that I can trace and debug from the execution of the Javascript in the browser, through the REST services, into the app logic and down into the DB. For me being able to step through the code from the JavaScript in the browser to the DB and back again is an amazing feature that I cannot live without now. It was the reason I switched to Netbeans on my friend recommending it to me based on that feature. Further the DTrace hooks are amazing, being able to see what is going on at every level provides another level of insight that I have not seen in other IDE's.

It crashes all the time.

We have never had this problem. We use Netbeans on OSX this may be a platform thing. I work with 10 to 15 freelancer at a time. We all use Netbeans and crashing has never been an issue.