The boat limits the chance of crossings.
The requirement of using the boat is meant to keep most wizards from being able to cross, while Voldemort himself would be able to cross just as easily in the boat as he would by flight. He crossed back from the lake quite easily when he used Kreacher to test the defenses of the cave.
“And then the Dark Lord sailed away, leaving Kreacher on the island …’
Harry could see it happening. He watched Voldemort’s white, snake-like face vanishing into darkness, those red eyes fixed pitilessly on the thrashing elf whose death would occur within minutes, whenever he succumbed to the desperate thirst that the burning potion caused its victim … but here, Harry’s imagination could go no further, for he could not see how Kreacher had escaped.
‘Kreacher needed water, he crawled to the island’s edge and he drank from the black lake … and hands, dead hands, came out of the water and dragged Kreacher under the surface …”
- Harry Potter and the Deathly Hallows, Chapter 10 (Kreacher’s Tale)
If flight was a possible method of crossing the lake, it would be more difficult to limit who could cross the lake. Making the boat the only possible way to cross limits other wizards’ capability to cross it. First of all, the boat is hidden in a way that few wizards would be capable of finding it.
“But why have they let us?’ asked Harry, who could not shake off the vision of tentacles rising out of the dark water the moment they were out of sight of the bank.
‘Voldemort would have been reasonably confident that none but a very great wizard would have been able to find the boat,’ said Dumbledore. ‘I think he would have been prepared to risk what was, to his mind, the most unlikely possibility that somebody else would find it, knowing that he had set other obstacles ahead that only he would be able to penetrate. We shall see whether he is right.”
- Harry Potter and the Half-Blood Prince, Chapter 26 (The Cave)
He also limited the boat to only be capable of carrying one qualified adult wizard.
“Dumbledore chuckled.
‘Voldemort will not have cared about the weight, but about the amount of magical power that crossed his lake. I rather think an enchantment will have been placed upon this boat so that only one wizard at a time will be able to sail in it.”
- Harry Potter and the Half-Blood Prince, Chapter 26 (The Cave)
Therefore, having the only possible way to cross the lake be the boat ensured certain limitations on who could cross without affecting Voldemort’s ability to cross the lake himself.
At that time, he may have not yet learned.
It is in no way certain that Voldemort knew how to fly when he hid the locket in the cave. Several years separate Voldemort’s creation of the locket Horcrux and the first known instance of his flying unaided. He acquired the locket as a young man.
“But before they were sure beyond doubt that the cup and the locket were both gone, the assistant who had worked at Borgin and Burkes, the young man who had visited Hepzibah so regularly and charmed her so well, had resigned his post and vanished. His superiors had no idea where he had gone; they were as surprised as anyone at his disappearance. And that was the last that was seen or heard of Tom Riddle for a very long time.”
- Harry Potter and the Half-Blood Prince, Chapter 20 (Lord Voldemort’s Request)
At the time he would have turned the locket into a Horcrux, he was still near the beginning of his path into further magical knowledge. For ten years after that, he disappeared from public view entirely, and used this time to further his knowledge.
“Ten years separate Hokey’s memory and this one, ten years during which we can only guess at what Lord Voldemort was doing …”
- Harry Potter and the Half-Blood Prince, Chapter 20 (Lord Voldemort’s Request)
He tells Dumbledore he has accomplished much since leaving Hogwarts, though he does not give details.
“I have come to you to ask that you permit me to return to this castle, to teach. I think you must know that I have seen and done much since I left this place. I could show and tell your students things they can gain from no other wizard.”
- Harry Potter and the Half-Blood Prince, Chapter 20 (Lord Voldemort’s Request)
During that time, he had experimented and tested the boundaries of magic. He may have continued to do similar experimentation with magic later into his life as well.
“Certainly,’ said Voldemort, and his eyes seemed to burn red. ‘I have experimented; I have pushed the boundaries of magic further, perhaps, than they have ever been pushed –”
- Harry Potter and the Half-Blood Prince, Chapter 20 (Lord Voldemort’s Request)
It is not known when exactly Voldemort gained the ability to fly unaided. At the time Quidditch Through the Ages was written, no method of flying unaided in human form was known. Presumably, this means that the wizarding public had not seen Voldemort take flight at the time Quidditch Through the Ages was written.
“No spell yet devised enables wizards to fly unaided in human form. Those few Animagi who transform into winged creatures may enjoy flight, but they are a rarity.”
- Quidditch Through the Ages
As it references a Quidditch game that was played in 1994, Quidditch Through the Ages was therefore published either in or after 1994. That means it had been published after Voldemort’s first rise to, then fall from, power.
“The exception to this general rule is Japan, where Quidditch has been gaining steadily in popularity over the last century. The most successful Japanese team, the Toyohashi Tengu, narrowly missed a win over Lithuania’s Gorodok Gargoyles in 1994.”
*- Quidditch Through the Ages
This does not necessarily mean that Voldemort only gained the ability to fly unaided after 1994, but it would mean that he was not flying publicly before then. Additionally, since he had not been out of Hogwarts for long when he created that Horcrux, and he spent many years after that increasing his knowledge and skill in magic, it should not be presumed that he already had the ability to fly unaided when he turned the locket into a Horcrux.