A couple of points to note. The first is that according to current theory, most of the energy in the Universe is not in fact in the form of nuclear particles. In fact 96% of the total energy is in the exotic forms we call dark matter and dark energy.
That aside, it is still true that there is far more energy in the form of familiar matter (neutron,protons,electrons mainly) than radiation today. The reason for this is that the energy of photons diminishes as the universe expands due to being redshifted. Formally the energy density of matter evolves with the size of the Universe (which we denoted by the 'scale factor' [tex]a(t)[/tex]) as:
[tex]\rho_m \sim a^{-3}[/tex]
If you think about this for a moment this is simply what you get by keeping the energy per particle constant, total number of particles constant but increasing the volume. So if we note the [tex]V \sim a^{3}[/tex] then the above expression becomes
[tex]\rho_m \sim \frac{1}{V}[/tex].
Now, for photons we also have the redshift. This means that the energy per particle does not stay constant, but changes as
[tex]E = E_0\frac{a_0}{a}[/tex]
this means that the energy density of radiation evolves as
[tex]\rho_rad \sim a^{-4}[/tex]
Since radiation energy density decays more rapidly with [tex]a(t)[/tex] than matter it means that even though initially there was more energy in radiation, the expansion of the Universe has caused there to now be much more energy density in matter.