(using middlegen preview downloaded from hibernate sourceforge; 
Middlegen-Hibernate-r4.zip)
When using MySQL the relations of the airline example is not detected. 
As a solution you should download middlegen from the middlegen website 
and extract the "mysql-connector-java-3.0.0-beta-bin.jar" from the 
archive and put that into the /lib/ directory. When you do that 
relations are getting detected.