First it's important to know what these folders actually do. Following are the workings of several of these files.
.settings -> This file records project specific settings and workspace preferences.
.bin      -> folder is usually where the compiled files are copied to.
lib       -> contains external libraries that are used in your project (like Apache Commons)
resources -> the resources like images, text, pdf, audio, video are usually copied here
src       -> the folder where the project's source files are located.
.classpath -> It contains information that the JDT feature needs in order to properly compile the project: the project's source folders, the output folders , and classpath entries.
.project  -> This file is maintained by the core Eclipse platform, and its goal is to describe the project from a generic, plugin-independent Eclipse view. 
So you can see that if you exclude some of the files like lib, resources, bin etc... Your jar file will probably stop working. Your jar file needs compiled files and their dependencies. 
For example: All your compiled .class files are in bin folder. And your jar works because of these .class files and NOT .java files that are in src. If you delete this bin folder then your jar will probably stop working.
Also, your project may be using some external library supplied by someone else. Like Apache Commons or google/guava and these are usually in lib folder. So you can't delete this folder as well.
However, if you no longer expect to use .java code, then you can exclude files that were created by eclipse to manage this project. See this post.
see also:
1. What's in an Eclipse .classpath/.project file?
2. exclude files from jar or war in eclipse