In Half Blood Prince Dumbledore said that apparating inside a house is rude, and usually wizards will have protection in place to prevent unwanted guests entering this way:
"Professor, why couldn't we just Apparate directly into your old colleague's house?" "Because it would be quite as rude as kicking down the front door," said Dumbledore. "Courtesy dictates that we offer fellow wizards the opportunity of denying us entry. In any case, most Wizarding dwellings are magically protected from unwanted Apparators. At Hogwarts, for instance —"
"— you can't Apparate anywhere inside the buildings or grounds," said Harry quickly. "Hermione Granger told me."
Why isn't the floo entry protected in the same way? In Chamber of Secrets Harry is able to enter Borgin and Burkes purely through accident. So it's logical that someone who wants to go there can probably do so even more easily. Why don't they have protection in place to avoid burgelers and police entering their shop unexpectedly through the floo?
It would seem that, unless a log of all the entry and exit through fireplaces is kept at the ministry, this would also be an easy way to let smugglers and unsupervised minors to enter their shop. Why isn't a protection against floo entrance, similar to protection against apparition, in place in wizarding houses?