At the end of Harry Potter and The Order of the Phoenix Fudge says following:
'Now see here, Dumbledore!' said Fudge, as Dumbledore picked up the head and walked back to Harry carrying it. 'You haven't got authorisation for that Portkey! You can't do things like that right in front of the Minister for Magic, you - you - '
This means that the creation of Portkeys is controlled by the ministry and creating one is if not a crime, at least a violation of some rule.
On the other side apparition is free - practically every adult wizard is allowed (and is able) to do it. There seems to be no restrictions for it. While it is not part of the standard classes in Hogwarts, the ministry does not do anything else to discourage people from learning it.
Why is that? Apparition seems to have shorter range than Portkeys but one can just repeat it and achieve more or less the same effect (unless you have a huge body of water to cross).