The article implies there was some conscious intent on the part of the government to deny Bill Gates his visa. Much more likely is that Gates' staff sent in a standard application through the Nigerian immigration department, the clerk looked at the forms - he doesn't know who this Bill Gates guy is - decided "hmmm... looks like this application is incomplete" and then sent it back with a big red rejection stamp on it.
No implied message on the part of the Nigerian government, just standard bureaucratic silliness.
You all know the old Napoleon quote.