Which user runs tomcat? Is it root, or is it a "tomcat" system user?
If it is root the export JAVA_HOME etc should be added in the /root/.bashc file
If it is a tomcat system user, you can add the env variables in the script you use to launch tomcat.
su - tomcat -c "export JAVA_HOME=...; /.../startup.sh"
However here I think the tomcat config may be the problem...
How did you install tomcat?