Because if the rail line cracks (which probably did appen in Japan), water floods into your tube. Then it becomes a question of "can they rescue you before your air supply ends" (since they would require an air supply for the vacuum)?
Oh, this post was in reply to the underwater part? Yes, I also think that this one isn't feasible for quite some time. My reply was in response to vacuum tubes over sea level. Right now we can't even have floating tubes anchored to the sea ground yet; storm waves rip every anchor we can build apart (it has been tried for wave power generators).
Vacuum tubes could probably be built deeper down where the waves aren't strong. I actually think that earthquakes wouldn't necessarily be a problem at that level, since everything would have to be quite flexible anyway. In order to elevate security, I could imagine making tube sectors detachable and having safety shutters. This way, if one sector is breached it could be sealed and detached such that it floats to sea level. The train could even be inside if you can control the pressure differences well enough to not kill everyone inside (something that is well understood for jet planes).
Since it's an interesting mindgame I thought about it a little further: There IS a hard problem to solve here: If your train takes 5min to stop from 4000km/h, its breaking distance would be 166km (assuming linear deceleration)! This means that you could only shut down sectors further away than 166km from the closest train - all sectors within are your vulnerable zone. That seams quite risky to me. On the other hand we do fly millions of people a year in pressure cabins with no way to escape. Since with this new system people's life would depend on tubes 160km long instead of 70m (length of a 747), all you need is materials that are 2000 times more reliable than those of our jet planes. While being emerged in seawater. And enduring a much higher pressure difference. Yeah.
I'd say let's wait and see what nanotechnology gives us :).