‘Level Six, Department of Magical Transportation, incorporating the Floo Network Authority, Broom Regulatory Control, Portkey Office and Apparation Test Centre.’ (OotP)
Well, Porkeys are indeed regulated by the Ministry, as shown above and in the following excerpts. It seems that all magical transportation means are part of a cluster of regulatory offices in the Ministry. Canon doesn't specify why Portkeys are so highly regulated, but it's apparently a major infraction to create one without authorization.
‘How’re we getting – wherever we’re going?’ Harry asked.
‘Brooms,’ said Lupin. ‘Only way. You’re too young to Apparate, they’ll be watching the Floo Network and it’s more than our life’s worth to set up an unauthorised Portkey.’
Order of the Phoenix - pages 50-51 - UK - chapter 3, The Advance Guard
He walked away from the pool to the place where the golden wizard’s head lay on the floor. He pointed his wand at it and muttered, ‘Portus.’ The head glowed blue and trembled noisily against the wooden floor for a few seconds, then became still once more.
‘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 –’
Order of the Phoenix - page 722 - UK - chapter 36, The Only One He Ever Feared
Portkeys as mass transit would be a nightmare to coordinate and provide on a continuous basis:
‘So, been keeping busy, Barty?’ said Bagman breezily.
‘Fairly,’ said Mr Crouch drily. ‘Organising Portkeys across five continents is no mean feat, Ludo.’
Goblet of Fire - page 84 - UK - chapter 7, Bagman and Crouch
'The whole Ministry’s been working on it for months [...] There have been two hundred Portkeys placed at strategic points around Britain, and the nearest one to us is up the top of Stoatshead Hill, so that’s where we’re headed.’
Goblet of Fire - page 66 - UK - chapter 6, The Portkey
If it took the Ministry -- who is authorized to create and distribute Portkeys presumably -- months to prepare two hundred Portkeys, and we know from the Quidditch World Cup that there are at least 100,000 witches and wizards in the world, it appears Portkeys would be impractical when it comes to implementation.
It seems that Portkeys are typically one-way and not round trip; the exception to this would be the Triwizard Cup (which, when you think about it, doesn't make a ton of sense. Why would Barty crouch Jr provide Harry with even the remotest means of escaping Voldemort?)
‘Morning, Basil,’ said Mr Weasley, picking up the boot and handing it to the kilted wizard, who threw it into a large box of used Portkeys beside him; Harry could see an old newspaper,
an empty drinks can and a punctured football.
Goblet of Fire - page 70 - UK - chapter 7, Bagman and Crouch
Portkeys as regular transportation, or mass transportation (since groups can use one Portkey), would increase the likelihood of Muggles accidentally picking up one and being transported. Technically, this would breach the International Statute of Wizarding Secrecy.
ETA: I have some more to add. Pottermore addresses the issue of why Portkeys aren't used as regular transportation. Logistical issues are addressed, as I mentioned above, but apparently a good amount of people are prone to "Porkey-sickness" which causes hysteria and nausea and, using Hogwarts as the example, had the hospital wing full to bursting with ill students during the first week of classes. If a fair number of people like that are prone to getting ill from using Portkeys, then they would be impractical for day-to-day use. [POTTERMORE - THE HOGWARTS EXPRESS]