Because print_r prints a readable version of your variable $media, which will be an array as per the documentation for get_media_embedded_in_content().
You see Array ( [0] => [youtube embed] ) in your browser because it’s rendering the HTML of the array element – if you check the source code of your page you would see something like:
Array (
[0] => <iframe src="..." />
)
But to answer your problem, you should print (or echo) with current() to get the “current” element in an array, which in this case will be the HTML for the first found media element (if one exists):
print current( $media );