Usually, they do not. Unless you make the case that the late fees were charged in error, you should expect to pay them.
Mortgage lenders normally only negotiate in short sale situations. They are motivated by the desire to avoid foreclosure. In a short sale, the lender will review the terms of the transaction and the net proceeds. If they are convinced that they will not make more by taking the property and selling it after foreclosure, they will accept a reduced payoff.
Now, that all said, we ARE in a different environment and new rules are being made to respond to the subprime crisis. It is entirely possible that some lenders may try new ways of avoiding foreclosure. So, ask away. Maybe you'll find a lender willing to negotiate fees.