No, but it's complicated
Please note that there are two types of prefixes described:
The name prefix, followed by ship's name. Indicates the origin/owner of the vessel. Examples:
- USS in USS Enterprise
- IKS in IKS Rotarran
The registry prefix, followed by ship's registry number. Indicates the type/purpose of the vessel. Examples:
- NCC in NCC-1701-D
- NAR in NAR-32450
- XCV in XCV-330
Ships with a name prefix USS from the pre-warp era on Earth belonged to the United States of America. The abbreviation stood for United States Ship. There was no Starfleet at that time, therefore it didn't mean that it was a Starfleet vessel, which gives a NO.
Post-warp era, pre-Federation era
The USS Enterprise (XCV-330) definitely has a USS prefix, however, it is not clear who was the owner of this spaceship. The ship was in service some time before 2143 and Starfleet was probably founded in mid-2130s. It is possible that the ship was owned by another entity, possibly United Earth.
All ships that had a USS name prefix at that time belonged to the United Federation of Planets. The abbreviation stood also for United Star Ship or United Space Ship.
It is a bit vague if all Federation ships belonged to Starfleet.
For example, the USS Raven was given to the civilian scientists by the Federation Council on Exobiology. It is unknown if the ship had ever been a Starfleet vessel (and was simply temporarily given to civilians), or was it a part of fleet that was not subject to Starfleet (but to UFP).
In a not completely canon Star Trek: Voyager Technical Manual we read that:
NAR (registry number) prefixes were among those used on vessels that were non-Starfleet but still under Federation jurisdiction.
USS Raven was designated as NAR-32450, which places it as a ship under UFP jurisdiction and outside of Starfleet. This gives an answer: NO.
Given that in the whole history in the Star Trek universe there were examples of starships who had a USS prefix but were not operated by Starfleet, the final answer has to be:
No, a USS name prefix does not imply a Starfleet vessel in 100%, but it is a good approximation.