As it seems there is no answer to my question due to technical reasons. It seems they still havent invented a system to have transparent background with video. SWF does support it for now so they are my only resort. If somebody finds another solution PLEASE let me know.
At the end my solution was a work around. For the Ipad I created flash content with a fallback of an image of the animation. This will mean that with other devices they will be able to see the animation but not with the animation itself. Therefore I created the following "solution":
<div id="flashContent">
<object classid="clsid:d27cdb6e-ae6d-11cf-96b8-444553540000" width="500" height="500" id="ani.rosa1">
<param name="movie" value="_swf/ani-rosa.swf" />
<param name="quality" value="best" />
<param name="bgcolor" value="#ffffff" />
<param name="play" value="true" />
<param name="loop" value="true" />
<param name="wmode" value="transparent" />
<param name="scale" value="showall" />
<param name="menu" value="true" />
<param name="devicefont" value="false" />
<param name="salign" value="" />
<param name="allowScriptAccess" value="sameDomain" />
<!--[if !IE]>-->
<object type="application/x-shockwave-flash" data="_swf/ani-rosa.swf" width="500" height="500">
<param name="movie" value="_swf/ani-rosa.swf" />
<param name="quality" value="best" />
<param name="bgcolor" value="#ffffff" />
<param name="play" value="true" />
<param name="loop" value="true" />
<param name="wmode" value="transparent" />
<param name="scale" value="showall" />
<param name="menu" value="true" />
<param name="devicefont" value="false" />
<param name="salign" value="" />
<param name="allowScriptAccess" value="sameDomain" />
<!--<![endif]-->
<img src="_swf/ani.rosa1.png" alt="Get Adobe Flash player" />
<!--[if !IE]>-->
</object>
<!--<![endif]-->
</object>
</div>