You have to specify it as shown below:
<warSourceDirectory>src/main/webapp</warSourceDirectory>
For step by step description please have a look at Maven GWT Plugin
Have a look at warSourceDirectory
Find sample pom.xml
at gwt maven war plugin configuration problem.
--EDIT--
try this one (replace as per your requirement)
<build>
<sourceDirectory>src/main/java</sourceDirectory>
<testSourceDirectory>src/main/test</testSourceDirectory>
<resources>
<resource>
<directory>src/main/resources</directory>
<excludes>
<exclude>**/*.java</exclude>
</excludes>
</resource>
</resources>
<plugins>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>2.3.2</version>
<configuration>
<source>1.6</source>
<target>1.6</target>
</configuration>
</plugin>
<plugin>
<!-- http://mojo.codehaus.org/gwt-maven-plugin/compile-mojo.html -->
<groupId>org.codehaus.mojo</groupId>
<artifactId>gwt-maven-plugin</artifactId>
<version>${gwtVersion}</version>
<executions>
<execution>
<configuration>
<extraJvmArgs>-Xmx640M -Xss1024k</extraJvmArgs>
</configuration>
<goals>
<goal>compile</goal>
<goal>eclipse</goal>
</goals>
</execution>
</executions>
<configuration>
<optimizationLevel>9</optimizationLevel>
<style>DETAILED</style>
<warSourceDirectory>src/main/webapp</warSourceDirectory>
<modules>
<module>com.x.y.z.EntryPointClassName</module>
</modules>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<version>2.3</version>
<configuration>
<webXml>src/main/webapp/WEB-INF/web.xml</webXml>
<warSourceExcludes>WEB-INF/lib/*.jar</warSourceExcludes>
</configuration>
</plugin>
...