How are you deploying?
Although the sysdeo plugin more accurately reflects a live Tomcat server environment than the WTP plugin, it doesn't have built-in deployment. You either have to copy the WAR to the Tomcat webapps directory or you need to add a context XML file to TOMCAT_HOME/conf/Catalina/localhost.
Of the two, I prefer the second option. Since my webapp projects are setup for
Maven builds, I create a webapp context whose docBase is something like $HOME/eclipse/workspace/mywebappproject/target/mywebapp.war.