Normally when eclipse try to find the files which are defined by your application..it links the src to src/main/java and src/main/resources..could you see the following entries in .class file of maven generated for eclipse..
<classpath>
<classpathentry including="**/*.java" kind="src" path="src/main/java"/>
<classpathentry excluding="**/*.java" kind="src" path="src/main/resources"/>
/**all repository entries are also here**/
</classpath>
then for the resources first the tomcat checks whether they are in the resources (and also checks them in the java folder)