Then some manual work I don't remember...
include_once("library/DrSlump/Protobuf.php");
include_once("library/DrSlump/Protobuf/Message.php");
include_once("library/DrSlump/Protobuf/Registry.php");
include_once("library/DrSlump/Protobuf/Descriptor.php");
include_once("library/DrSlump/Protobuf/Field.php");
include_once("gtfs-realtime.php");
include_once("nyct-subway.php");
include_once("library/DrSlump/Protobuf/CodecInterface.php");
include_once("library/DrSlump/Protobuf/Codec/PhpArray.php");
include_once("library/DrSlump/Protobuf/Codec/Binary.php");
include_once("library/DrSlump/Protobuf/Codec/Binary/Reader.php");
$fm = DrSlump\Protobuf::decode('transit_realtime\FeedMessage',file_get_contents( ... URL to gtfs file here ... ));
Then I walked it to get what I needed.