JBoss Tools does not know about your jboss-as:deploy setup out of the box.
It only publishes what is in your project - is web.xml inside your project or generated by jboss-as:deploy ?
Have you tried importing the project as a Maven project so m2e-wtp (maven integration for WTP that jboss tools uses) will try read your maven settings and deploy similar to what mvn jboss-as:deploy does ?