Are Cosmic Rays net neutral in charge? As I understand them, Cosmic rays mainly consist of high energy charged particles. I began to wonder if they would eventually net charge the Earth and then assumed that they must  come in roughly equal amounts of charge. If they don't I suppose the charged Earth would deflect like charge particles and attract the opposite until it is neutral once more. Any thoughts on the matter would be interesting to hear.
 A: 
As I understand them, Cosmic rays mainly consist of high energy charged particles. 

Yes, roughly 90% of all cosmic rays (CRs) are protons, another 9% are alpha particles and the remaining 1% are electrons, positrons, and heavy nuclei. Most of these are in the 1-10 GeV range, dropping off at $N(E)\sim E^{-2}$ from thereon out (this Physics.SE post shows the common CR spectra).

I began to wonder if they would eventually net charge the Earth ... If they don't I suppose the charged Earth would deflect like charge particles and attract the opposite until it is neutral once more

If an over-abundance of positively charged CRs developed, they would start deflecting the same positively charged CRs & attracting the negatively charged CRs; similarly the other way around. Thus, our planet & atmosphere remains roughly quasi-neutral (though, as seen in this Physics.SE post, there is a 500 kC charge on the surface). 
The charge however, is related more to the internal processes and the solar wind than galactic/extra-galactic CRs accumulation. For this aspect of earth's charge, see this Physics.SE post. At energies less than ~ 10 GeV, the solar wind will actually be able to deflect the CRs away from earth (hence the slight down-tick on the CR spectrum linked in the top paragraph). At higher energies, the solar wind cannot do this, but the particles come more infrequently (ranging between 1 particle per square-meter per second down near 100 GeV to 1 particle per square-kilometer per century around $10^{21}\,\rm eV$) so the fewer particles would not really affect the electric field.

... then assumed that they must come in roughly equal amounts of charge.

Not at all. As I stated above, the vast majority are single protons and only a small fraction are electrons. As an aside, the electron-positron anisotropy is a somewhat hot topic in CR Astrophysics (cf. this ADS search of electron positron anisotropy).
We believe that the bulk of galactic CRs are produced in galactic supernova remnants (see also this post of mine for CR protons producing neutrinos). Models produced by the leaders of the field (e.g., Ellison et al and Jones & Kang) show that the ratio $N_p/N_{e^-}\sim10^{-4}$ exist at the sources before diffusing out into the galaxy, matching what is found in the observatories (as it should, assuming a steady-state production of CRs).
A: The net charge of earth due to incoming CR particles may not be static and may vary over periods of time. Earth may have a semi-stable ferromagnetic core and transient peaks of positive or negative absolute-earth-charge may inductively contribute to earth’s magnetic pole reversal. Assuming CR particles with directed energy, if earth is bathed in positively charged CR particles the earth should take on a positive charge or a negative charge for the opposite scenario. Significant static-attraction or static-repulsion of CR particles due to earth’s accumulated charge may only occur at the extremes of Earth’s transient potentials (magnitude of potential extremes would then depend on the typical velocity and mass-to-charge ratio of the particles). Periods of the transient extremes may be similar to the periods of Earth magnetic pole reversals. 
