Charmonium suppression in hot and dense nuclear matter has been argued to be a signature for the production of the quark gluon plasma (QGP). In order to search for this effect in heavy ion collisions one must have a clear understanding of all the factors that can contribute to such a suppression. These may include shadowing of the partons in a nuclear environment, breakup of a correlated $c-bar{c}$ pair as it traverses the nuclear fragment, suppression of feed-down from higher mass states as well as other initial state interactions. In order to disentangle these effects one must measure charmonium production rates in both proton+proton (p+p) and proton+nucleus (p+A) collisions. The p+p collisions serve as a baseline for searching for suppression compared to binary scaling predictions, allow one to quantify the amount of feed-down from higher states as well as serve as a tool to distinguish between different theoretical calculations for charmonium production mechanisms. In order to quantify nuclear effects it is also necessary to study charmonium production in p+A collisions where the temperature and density of the system are low compared to a heavy ion collision. These measurements allow one to determine the influence of nuclear shadowing and breakup in cold nuclear matter which can be extrapolated to heavy ion collisions in order to determine the amount anomalous suppression. Of course, extrapolations that rely on a model based technique depend heavily on the assumption of a production mechanism, a fact that reinforces the importance of the p+p measurements...
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