First, I'm sure he got permission to use those readers' names in print. In most cases, newspapers have policies where if a person writes to a newspaper, the newspaper must get permission to run that information. Or the reader can request his/her correspondence not see print. Or there may be a general assumption that if you submit your name, your correspondence/name can be used.
Second, JJT writes for a national newspaper. He has a right to criticize by virtue of his position. The athletes know this and so do the coaches. They may not like it, but that's what occurs in a country with a free press.
Third, if the 49ers or any other team doesn't adopt the strategy that the Commanders, Giants and every other team this side of San Francisco did in bumping T.O. and putting a safety overtop, then T.O. is going to burn them all day. But don't expect in upcoming games for T.O. to receive the generosity that the 49ers showed.
I'm sure if T.O. has big games against the Steelers, the Giants, the Ravens and the Eagles, then JJT will recant his statement.
But one game doesn't not prove T.O. hasn't slowed down. Any receiver of above-average talent could have beaten the double coverage the 49ers played. See Randy Moss and the Dolphins game for example.