There are two easy options you can try:
1) Load the Shapefile natively in Flex using vanrijkom classes. Read the geometries and create overlays for the mapping api.
2) Process them in PHP using the ShapeFile.inc.php class developed by Juan Carlos Ulloa, send them, using AMFPHP, as AS3 objects using similar to the mapping API and overlay.
I have tried both ways now. You can check the code of the first try and a demo at:
I am still not sure which way I am gonna take for BiodiversityAtlas as both look fine to me. I probably will use the PHP way as in any case, if the user has to upload the file to the server then I can process i there anyway and I might store them directly on PostGIS even before displaying... so that looks my router.
But in any case is great to see I can go both ways and that both are surprising fast.
If anybody is interested on the PHP example please let me know.