As with all investigations of pre-Socratic thinkers, conjectures will remain tentative, due to sketchy textual sources.
Perhaps they saw energy in terms of powers which objects have, making the objects — i.e., matter — primary, and energy secondary.
When the Milesians sought a unifying principle, they looked to matter instead of to energy — what is the common principle behind all matter? — although they were aware of forces, as Leonard Susskind writes:
Of all the forces of nature, only three were known to the ancients — electric, magnetic, and gravitational. Thales of Miletos (600 BC) was said to have moved feathers with amber that had been rubbed with cat fur. At about the same time he mentioned loadstone, a naturally occurring magnetic material. Aristotle, who was probably late on the scene, had a theory of gravity, even if it was completely wrong. These three were the only forces that were known until the 1930s.
The history of physics changed direction at some point placing more emphasis on energy as an independent topic, rather than energy as merely a property of, or an ancillary to, matter.
So it is that post-Socratic and post-Newtonian physics seeks a Grand Unified Theory (GUT), not uniting all matter, but uniting all known forces. Physics as a discipline decided that it had worked about the basic principle of matter — all atoms are composed of electrons, neutrons, and protons, etc. — and turned to energy.
The ancients knew of the three main forces because they were clearly observable, as Leonard Susskind notes:
What makes these easily observed forces special is that they are long-range. Long-range forces fade slowly with distance and can be seen between objects when they are well separated.
While physicists search for a GUT, they focus primarily on electro-magnetic and nuclear forces. A further step would make a truly universal system by including gravity. This is called a ‘Theory of Everything’ (TOE).
While GUT and TOE remain speculative and controversial, they are also a continuation of the Milesian reductionist project, with a shift toward energy and away from matter.
While gravity is the most easily observable force, and therefore the first object of philosophical speculation, it is also the weakest force. This is counterintuitive to the extent that it is everywhere visible and to the extent that someone who’s had a brick dropped on his toes will not consider the force to be empirically weak.
Yet gravity is considered to be a weak force because for any one unit of matter, the measured force is small relative, e.g., to magnetic forces. Gravity’s force seems strong, exerting hundreds of pounds of force on each human being, because the earth’s mass is so large. By contrast, a magnet of much smaller mass than the earth would be able to exert an equal or greater force.
Gravitational force is by the far the most obvious of the three, but surprisingly it is much weaker than electromagnetic force. The reason is interesting and worth a short digression. It goes back to Newton’s universal law of gravitational attractions. Everything attracts everything else.
In the search for universal principles — whether GUT or TOE or the Milesian reductionist project — language is strained to capture the concepts. Is this the systemic principle that’s “behind” or “underneath” all reality? The prepositions betray language’s difficulties in capturing the idea: most prepositions are spatial, and yet the quest here is not for a primarily spatial relationship.
In sum, while the Milesians made significant progress toward a unifying principle which underlies all reality, their search seems to have been skewed toward matter at the expense of energy.