If you want to generate objects for a table that has a public synonym, you should actually generate the objects against the real table - and then change the table name at runtime. Ibator supports this automatically.
For example, assume there is a public alias "FRED" that points the the table "HR.EMPLOYEES". The following table configuration will generate the objects based on HR.EMPLOYEES, but the runtime SQL will only refer to FRED:
<table schema="HR" tableName="EMPLOYEES">
<property name="ignoreQualifiersAtRuntime" value="true" />
<property name="runtimeTableName" value="FRED" />
</table>