Either do the impossible…
Purely as written, the game presents readers with a contradiction. The description of the figurine of wondrous power (ebony fly) in Pathfinder tells readers that "an ebony fly is the size of a pony and has all the statistics of a pegasus." Those two things can't simultaneously be true, and the description offers no exceptions or advice on how to facilitate meshing these competing truths.
To be clear: If the animated ebony fly is the size of a pony then it does not have all the statistics of a pegasus: a pony is Medium, a pegasus is Large, and size is a statistic. If taking literally the animated ebony fly's description, you as the GM need to rule that either the animated ebony fly is Medium and adjust the pegasus statistics, or it's Large and that the size of a pony is a metaphor, or it's some horrifying, chaotic compromise between the two (and I have no idea how that works because the game doesn't do typically that). Until you make such a ruling, Schrödinger's ebony fly remains in a quantum state, functionally unknowable.
Personally, I find the idea of the size of a pony as metaphor both in keeping with tradition and playable.
…Or embrace the metaphor
I don't suggest taking literally that the animated ebony fly is pony-sized. Instead, I think this is just a matter of tradition butting against contemporary technology. See, the animated ebony fly has been the size of a pony but that's been (ahem) largely meaningless since well before the advent of hyperlinks. The phrase dates back at least to the Dungeon Master's Guide (1979) for Advanced Dungeons & Dragons wherein the figurine of wondrous power (ebony fly), when animated, "grows to the size of a pony" then has unique statistics (144). A similar description of the animated ebony fly is repeated in its Encyclopedia Magica (1999) entry (478) for Advanced Dungeons & Dragons, Second Edition, the animated ebony fly there also having unique statistics. It took the Dungeon Master's Guide (2000) for Third Edition to put the animated ebony fly description into its present form (on page 116 or here, and, after the 3.5 revision, 256 or here). Then the Pathfinder Core Rulebook (2009) changed the animated ebony fly from having the statistics of the hippogriff to those of the pegasus but left the remainder of the description unchanged (513).
I put this all together as meaning that a Pathfinder reader should imagine that an animated ebony fly is the size of typical IRL pony, but it is mechanically—for game purposes—just a reskinned pegasus with no attacks. Although the site does a lot of things very well, it's the d20PFSRD site that added to the animated ebony fly description the hyperlink to pony, and I think that was a mistake (cf. the entry on Archives of Nethys). Absent that hyperlink—which obviously isn't in the Pathfinder Core Rulebook—the phrase the size of a pony is much more clearly (but certainly not completely clearly) a metaphor… and also an example of the relatively common and sometimes frustrating combination of fluff and crunch that's present in many d20 System games and, really, roleplaying games generally.
With all that in mind, I really don't think Pathfinder (or D&D 3.5) is using pony as a unit of mechanical measure in its description of the animated ebony fly, and when I GM I resolve this answer's opening contradiction by using no-attacks pegasus statistics and just describe the animated ebony fly as being roughly as big as a pony, picking the word big because of its lack of mechanical baggage. So far as I'm aware, my campaigns haven't suffered because I resolved things this way.