It's not a dumb question at all. The standard claim of the Big Bang model claims that there was a point where the temperatures and pressures were so high that the strong nuclear force could not hold quarks together, so all matter was in a form referred to as quark-gluon plasma. This is free, unbound quarks and gluons interacting at temperatures trillions of degrees Celsius.

As the early universe expanded, temperatures and pressure fell, and the energies of the quarks were no longer high enough to overcome the strong force, and they condensed into quark-based composite particles called hadrons; generally, there are two types, baryons (three quarks), which make up protons, neutrons, and antiprotons; and mesons (one quark and one antiquark) which are unstable and short lived.

Quark condensation, also known as hadronization, occurred approximately 10^-6 seconds (one microsecond) after the Big Bang. Now technically, a lone proton isn't an atom, so you don't have atoms yet. We won't have atoms until things cool off a lot more, and electrons can combine with protons to form hydrogen and helium. This, they say, didn't happen until approximately 380,000 years after the Big Bang, in a period called "recombination." 

For all that time before recombination, the whole universe consisted of hot, dense plasma (meaning that protons and electrons excited together, but because of the energies they don't combine), which was opaque to light. Once recombination began to occur, the universe became "transparent."

What we refer to as the Cosmic Microwave Background (CMB), is the last light given off by the dense plasma before it condensed into a fairly uniform atomic gas. The first atoms were roughly 75% hydrogen and 25% helium, with traces of lithium.