One example is YouTube; they lost huge buckets of money in their entire independent existence, until Google's acquisition completely changed the economics of their bandwidth costs. Would they have been able to become profitable if they stayed independent? Maybe!
Another one (perhaps clearer) is Broadcast.com. Never turned a profit in their independent existence; never turned a profit for Yahoo after acquisition, either.
Interesting side or foot-note was that myspace went from 600m to 50m, first purchases (enabling vcs to exit) and then disposed of (by its BigCo purhaser) after not monetizing.
http://www.quora.com/How-profitable-is-BitTorrent-Inc
"Our main source of revenue is off the toolbars we push out, which isn't a great source of monetization, but it's something. You can do the math on how many installs we have and what the monetization of toolbars is, and subtract out the costs of having 50 employees, and you'll get a reasonable ballpark of how profitable we are, although the short answer is very. Even lousy monetization works well when you have more users than Twitter."