Posting all the lyrics, so it'll be easier for everyone.

"We sent out the SOS call.
It was a quarter past four in the morning when the storm broke our second anchor line.
Four months at sea,
Four months of calm seas
Only to be pounded in the shallows off the tip of Montauk Point.
They call them rogues,
They travel fast and alone.
On hundred foot faces of God's good ocean gone wrong.
What they call love is a risk,
'Cause you will always get hit out of nowhere by some wave and end up on your own.
The hole in the hull defied tthe crew's attempts to bail us out.
And flooded the engines and radio and half buried bow.
Your tongue is a rudder.
It steers the whole ship.
Sends your words past your lips or keeps them safe behind your teeth.
But the wrong words will strand you.
Come off course while you sleep.
Sweep your boat out to sea or dashed to bits on the reef.
The vessel groans the ocean pressures its frame.
Off the port I see the lighthouse through the sleet and rain.
And I wish for one more day to give my love and repay debts.
But the morning finds our bodies washed up thirty miles west.
They say that the captain stays fast with the ship through still and storm.
But this ain't the Dakota, and the water is cold.
We won't have to fight for long.
This is the end.
This story's old but it goes on and on until we disappear.
This is the calm
Calm me and let me taste the salt you breathed while you were underneath.
I am the one who haunts your dreams of mountains sunk below the sea.
I spoke the words but never gave a thought to what they all could mean.
I know that this is what you want.
A funeral keeps both of us apart.
You know that you are not alone.
Need you like water in my lungs.
This story's old but it goes on and on until we disappear.
This is the calm
Calm me and let me taste the salt you breathed while you were underneath.
I am the one who haunts your dreams of mountains sunk below the sea.
I spoke the words but never gave a thought to what they all could mean.
I know that this is what you want.
A funeral keeps both of us apart.
You know that you are not alone.
Need you like water in my lungs.
This is the end."

Anyways. My own interpretation would lead me to believe that this song has two meanings. A literal one and a metaphorical one. Literally, the whole song goes into a shipwreck and the two who are in love end up drowning. That is where the funeral part would come in. Metaphorically, I think it would mean that their love for eachother has died (funeral for their relationship, maybe?) and they are not able to rekindle it, so they are apart.

Also I came across this when I was looking for lyrics. Here are what some other people would say on this website : http://www.songfacts.com/detail.php