There are certain file content types that require non-trivial generic processing. For instance, an XML file should be parsed. Integration Server supports registering ContentHandlers to perform this generic processing.
There are a number of different ways into the Integration Server. HTTP POST, Email, FTP, etc. The HTTP or MIME Content-Type header is used to figure out which ContentHandler to run on the input. The FTP file extension is used (along with the lib/mime.types file) to figure out what ContentHandler to run on incoming FTP files.
Generally there isn’t anything generic that can be done to a file of text/plain type, so the default ContentHandler is used. That handler just puts the stream in the pipeline and the service can do whatever processing it wants to on the incoming data. For many file types this is exactly what you want (that message is not an error, just informing you that the default ContentHandler was used).
BTW, there is an example of an implementation of a ContentHandler in the WmSamples package.