If the .project and .classpath are already committed, then they need to be removed from the index (but not the disk)
git rm --cached .project
git rm --cached .classpath
Then the .gitignore would work (and that file can be added and shared through clones).
For instance, this gitignore.io/api/eclipse file will then work, which does include:
# Eclipse Core
.project
# JDT-specific (Eclipse Java Development Tools)
.classpath
Note that you could use a “Template Directory” when cloning (make sure your users have an environment variable $GIT_TEMPLATE_DIR set to a shared folder accessible by all).
That template folder can contain an info/exclude file, with ignore rules that you want enforced for all repos, including the new ones (git init) that any user would use.
As commented by Abdollah
When you change the index, you need to commit the change and push it.
Then the file is removed from the repository. So the newbies cannot checkout the files.classpathand.projectfrom the repo.