I have been trying unsuccessfully for the last few days to run Cobertura 2.4 with Maven 3.0.2. We have a very large project with many modules (sub-projects). What I found is
In maven 3.0.3 (not yet out when you asked the question), simply use maven's site plug-in and configure it such that it uses cobertura, as follows:
org.apache.maven.plugins maven-site-plugin 3.0 org.codehaus.mojo cobertura-maven-plugin 2.5.1 html xml ....