You have to init the db once for Flyway. That is when Flyway creates the table used to track the migrations. As you have noticed, any attempt to init again fails because the table already exists.
I suggest making a separate ant task that calls Flyway's init that you can run manually to initialize Flyway, something along the lines of:
<target name="init-flyway">
<path id="flyway.lib.path">
<fileset dir="./lib">
<include name="**/flyway*.jar"/>
</fileset>
</path>
<path id="flyway.classpath">
<fileset dir="./lib" includes="ojdbc6-11.2.0.3.jar"/>
</path>
<taskdef uri="antlib:com.googlecode.flyway.ant"
resource="com/googlecode/flyway/ant/antlib.xml"
classpathref="flyway.lib.path"/>
<flyway:init driver="oracle.jdbc.OracleDriver"
url="jdbc:oracle:thin:@localhost:1521:WBMD"
user="system"
password="manager"
initVersion="0"
initDescription="Version table initialization (table "USERNAME"."schema_version" )"/>
</target>