In Harry Potter and the Half Blood Prince, what did the Ministry do to increase the protection around Hogwarts, apart from stationing Aurors at Hogwarts?
Possibly more protective charms were put up.
When Harry gets off the train Tonks takes him to the entrance of Hogwarts and they have a conversation in which Tonks mentions the security.
"I could climb a wall," he suggested. "No, you couldn't," said Tonks flatly. "Anti-intruder jinxes on all of them. Security's been tightened a hundredfold this summer."
- Harry Potter and the Half Blood Prince, Chapter 8 (Snape Victorious)
To me this suggests the addition of more protective charms/jinxes being added to the Hogwarts perimeter, due to the implication of Anti-intruder jinxes being added.
The magical protection around Hogwarts itself was strengthened.
The Minister of Magic, Rufus Scrimgeour, explained in a news article how the Ministry would be protecting Hogwarts. Though he doesn’t go into details, someone confirmed that the new security measures for Hogwarts would include defensive spells and charms, and counter-curses, in addition to the team of Aurors that would be stationed around Hogwarts.
“For obvious reasons, the Ministry will not be going into detail about its stringent new security plans,’ said the Minister, although an insider confirmed that measures include defensive spells and charms, a complex array of counter-curses and a small task force of Aurors dedicated solely to the protection of Hogwarts School.”
- Harry Potter and the Half-Blood Prince, Chapter 3 (Will and Won’t)
Dumbledore also says the magical protection around Hogwarts was strengthened over summer.
“The castle’s magical fortifications have been strengthened over the summer, we are protected in new and more powerful ways, but we must still guard scrupulously against carelessness on the part of any student or member of staff.”
- Harry Potter and the Half-Blood Prince, Chapter 8 (Snape Victorious)
So, the protection included strengthening the magical protection surrounding Hogwarts as well.
In addition to the other answers, all mail in and out of Hogwarts was being checked:
"All the owls are being checked too," said Hermione.
"But I thought all the owls were being searched. So how come these girls are able to bring love potions into school?"
While it does not explicitly state that it was the Ministry that was checking the mail, we know that during the same time period the Weasleys' mail was getting checked as well, and there it is explicitly stated that it was being checked by the Ministry:
These measures have caused a certain amount of inconvenience to Arthur and Molly – all their post, for instance is being searched at the Ministry before being sent on.
"Can't be anything dangerous, all our mail's still being searched at the Ministry," replied Ron, though he was eyeing the parcel suspiciously.