If, like me, you arrived here searching for a way to exclude generated sources from checkstyle, do this:
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-checkstyle-plugin</artifactId>
<version>2.15</version>
<configuration>
<sourceDirectory>${project.build.sourceDirectory}</sourceDirectory>
</configuration>
</plugin>
By default, the checkstyle:checkstyle goal of the checkstyle plugin uses ${project.compileSourceRoots}, which apparently includes generated source directories.
If you change it to ${project.build.sourceDirectory}, it will use only the source directory, not any generated source directories.
Note that while <sourceDirectory> is deprecated, the alternative, <sourceDirectories>, does not appear to work.
Edit: In comments, @Cyrusmith, @Ben, and @Olivier Callioux report that as of 2017, <sourceDirectories> works; I cannot confirm.