Someone asked the same question here [1] and this seems to be an open issue.
The solution I found was to use the 'copy-resources' goal from maven-resources-plugin [2] including only the .xsd files.
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>jaxb2-maven-plugin</artifactId>
<version>1.5</version>
<executions>
<execution>
<id>schemagen</id>
<goals>
<goal>schemagen</goal>
</goals>
</execution>
</executions>
<configuration>
<includes>
<include>**/*.java</include>
</includes>
<outputDirectory>${project.build.directory}/generated-resources/schemas</outputDirectory>
</configuration>
</plugin>
<plugin>
<artifactId>maven-resources-plugin</artifactId>
<version>2.6</version>
<executions>
<execution>
<id>copy-resources</id>
<phase>process-resources</phase>
<goals>
<goal>copy-resources</goal>
</goals>
<configuration>
<outputDirectory>${project.build.outputDirectory}/META-INF/schema</outputDirectory>
<resources>
<resource>
<directory>${project.build.directory}/generated-resources/schemas</directory>
<includes>
<include>**/*.xsd</include>
</includes>
</resource>
</resources>
</configuration>
</execution>
</executions>
</plugin>
[1] http://mojo.10943.n7.nabble.com/Maven-Jaxb2-plugin-schemagen-generating-classes-td40005.html [2] http://maven.apache.org/plugins/maven-resources-plugin/examples/copy-resources.html