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When you watch Star Trek: Enterprise you see them communicating with Starfleet command, Admiral Forrest is a recurring character.
It seems to me that the admiralty and command structure is very established but Enterprise was the first deep space vessel. How did Starfleet build its command structure and flag officers if no one has "boldly been there before?"
The "Starfleet" that we see in Enterprise was evolving out of the United Earth Space Probe Agency, which was an international agency set up after Earth's Third World War. It served the same role that NASA does today, but wasn't tied to any one nation or faction.
The UESPA had a long history with aeronautics and space travel (with very limited warp capability, using warp drives similar to Zefram Cochrane's Phoenix) for almost a century before the NX project that Forrest and Archer were involved with.
There was already a fleet, consisting of terrestrial aircrafts, short-haul spacecrafts, ambassadorial vessels with low warp capability (for transporting diplomats to Vulcan, for example), and both automated and one-man deep space probes.
By the 2130s, UESPA had been integrated with Starfleet as the leading United Earth space exploration service. Together, UESPA and Starfleet accomplished many missions. (ENT : "First Flight")
(Source)
Note that the NX-01 was not constructed until 2150.
In short, there was already a fleet for Forrest to be an admiral in. It's only that the focus of Enterprise happens to be on the NX vessels — being experimental, there were only a few of them. This gives the illusion to the viewer that there is "no fleet".
It had a fleet. A small one. NX-01 was special not because it was their first ship, but because it was the fastest, first to get to Warp 5.0, thus it was the first capable of speed high enough to commence reasonable deep-space missions. And note that deep-space doesn't mean "outside of solar system", but further. There already was a number of ships doing trade with other systems. Additionally, Starfleet was for all non-private Earth vessels, not just the ones that went to deep space.
There were already other vessels in existance, not many, but still. USS Intrepid comes to mind, it was a semi-military (every time we see it it's doing a militaristic task, either battle, defence or patrol) vessel dedicated to defending the planet, and it had at least one sister ship which name escapes me (two sister ships, if we go by the scenes in ENT: "The Expanse".
And then there were a bunch of freighters and transports (including diplomatic - how do you think they make the trips to the embassy on Vulcan? They didn't ask Vulcans for a lift every time) and experimental ships (many of which we see, either during "NX-01 in the drydock once again" scenes or dring Captain Archer's flashbacks, like in ENT: "First Flight", some of which probably answered to Starfleet. I doubt they'd hire private contractors for maintaining their orbital shipyards (there were more than one. NX-01 was being repaired and Columbia was being built at the same time).
Besides, even if there were no other ships, it helps to have a complete, working command structure for an organisation that is already building the fleet up and has to cooperate with foreign power. It's not unheard of on our planet in real life.
tl;dr: There is no reason to assume that a fleet of ships must exist to have people in the rank of "admiral".
Out-of universe, the depiction of the organization Starfleet was inspired by the U.S. Navy. This included duplicating the rank system that seems to be in use there, as well as a random selection of other customs when the situation seemed fitting.
In universe, however, there is no reason to assume that Starfleet must be a total copy of the current navy. As could be seen through the shows, Starfleet's rank structure was mostly used as a hierarchy that primarily indicated command priority and less so fixed positions. The commanding officer of an individually operating Starfleet spacecraft often holds the rank of Captain, but sometimes also Commander or Admiral. The first officer often is a Commander, but sometimes also a Lieutenant Commander or a Captain. And so on. Along these lines, an Admiral is simply a member of Starfleet occupying a higher rank than a Commodore, without any implications of having to have an active fleet.
Even if early Starfleet did not have any ships (which does not need to be the case; they may well have sublight or low-warp ships, just not interstellar explorers capable of reaching warp 5), there is no issue. Given the huge undertaking that starting to bridge interplanetary distances is, an organization needs a setup phase. In that phase, much preliminary work already needs to be done, and with Starfleet being a research organization with some military undertones, all the staff at that time already needs to be organized in a ranking structure. It may be comparable with a newly founded enterprise that has yet to finish the design of their very first product (still living on the initial fund, for instance) and already has a CEO or a director - probably even a marketing director, even though the company is not actively selling anything yet.
To reiterate, and explicitly answer the question:
How did Starfleet build its command structure and flag officers if no one has "boldly been there before?"
Starfleet copied the rank structure (maybe "rank sequence" is a less misleading term?) of the current U.S. Navy. It then started employing people, and based on their successful contributions to the organization, they got promoted step by step through those ranks, starting as Ensigns, and gradually moving towards the rank of an Admiral.
TL;DR: The Starfleet command structure & rank system was based on the existing naval ranks.
Starfleet and its predecessor, The United Earth Space Probe Agency (UESPA), evolved from existing organizations like NASA. As of the NX Project in 2143, the organization was still fairly new (only 20 years old) and did not have an admiralty yet. Starfleet indeed had an existing fleet of warp-capable vessels, although none could yet exceed Warp 2.0. In fact, exceeding that limit was the very goal of the project.
Commodore Maxwell Forrest was one of the three highest-ranking individuals in Starfleet, and was personally overseeing the NX project. When the NX-01 made the project viable and was sent off on its mission, it became essentially the symbol of what Starfleet was all about. As a result, Forrest was promoted to the rank of Admiral and effectively given control of Starfleet as its top administrator.
Note: NASA does not currently have its own rank system (the NASA command structure is based on mission roles), but typically recruits from within the US Navy and Air Force. As a result, the vast majority of astronauts have pre-existing military ranks such as Lieutenant, Major, Colonel, etc.
