Version 2.1 of the plugin is broken and always reports 100% coverage. Be sure to specify version 2.0.
<project> ... <reporting> <plugins> ... <plugin> <groupId>org.codehaus.mojo</groupId> <artifactId>cobertura-maven-plugin</artifactId> <version>2.0</version> </plugin> </plugins> </reporting> ... </project>
If you are running cobertura:cobertura from the command line, it takes the version from the build section instead.
You can check which version you are using with mvn help:describe -Dplugin=cobertura
Make sure to delete any cobertura.ser files before trying again