Only the "highest" files in the cascading filesystem are whitelisted for code coverage.
To test your module's file, remove the higher file from the cascading filesystem by disabling their respective module.
A good way of testing is to create a "vanilla" testing environment for your module, devoid of anything that isn't required by the module.
Try the following:
phpunit {bootstrap info} --coverage-html ./report {insert path to tests.php}
. If any error messages show up, fix them and try to generate the report again.