Suppose you have such input parameter in your flow definition and you want 'true' to be default value:
<input name="myFlag" type="boolean"/>
Then define some action state as initial state (<flow start-state="myFirstState">) and set default value there:
<action-state id="myFirstState">
<on-entry>
<set name="myFlag" value="myFirstState==null?true:myFlag"/>
</on-entry>
...
<action-state>
This would do the trick.