Sorry but Frank was cool, now he is to old for this new world. 
He was punched by a kid, kicked in the balls by Deathstroke, make a X-over with Archie. 
And you still ask how?

Pick up the comic. It's worth reading, and I don't even like Daken. Or I can summarize what happened for you.

By cutting him up like sausage

horrible writters...............  frank 4 ever 

Frank died on that rooftop for me, and that was that.

Perhaps there was a missing panel in which Daken showed him the Dolph Lundgren Punisher movie and it weakened him so much it made him able to be defeated!

no matter what you think, Frank is still just a guy....a crazy guy but just a guy....doesn't matter what kind of training he has there was no way he was going to win that fight....that fight was probably the most realistic fight that Frank's ever had with a superhuman

"that fight was probably the most realistic fight that Frank's ever had with a superhuman "

Contrary to popular bleef, Punisher is actually Bruce Wayne.  He is like herpes in a way.  He may be gone for a while, but some version of him, even a slightly nastier version of him, it'll be back.

it's all an bad dream