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
I successfully integrated Cobertura in my projects with adding this:
  
    
      
        org.codehaus.mojo 
        cobertura-maven-plugin 
        2.4 
        
          
            
              foo/bar/**/*.class 
             
           
         
    
      
        clean 
        pre-site 
        
          clean 
         
       
      
        instrument 
        site 
        
          instrument 
          cobertura 
         
       
     
       
     
   
  
    
      
    
    org.codehaus.mojo 
    cobertura-maven-plugin 
    2.4 
    
      
        html 
        xml 
       
      
       
     
   
If you run mvn cobertura:cobertura the reports will be generated in target\site\cobertura. See also maven cobertura plugin.
Today I analyze projects with SonarQube. It has an easy installation step (if you are not interested in using an enterprise database) and also includes a code coverage analysis (using JaCoCo) among many other metrics.