Briefly, its all to do with the solubility, stability and dissolution rates in the body of the drug in question.
These three factors affect the way in which the drug is absorbed, distributed and excreted.
Hydrochloride salts of drugs meet these criteria more readily than other salts and consequently, there are more hydrochloride salts found in the various pharmacopoeias than any other.
All the same, on rare occasions hydrochlorides are not the best choice. One drug that comes to mind is Propoxyphene, which has been widely used in combination with aspirin in the USA. The Propoxyphene was in the form of the hydrochloride, but it was eventually found to be unstable in combination with aspirin. The Propoxyphene was then reformulated as the napsylate salt and was found to be perfectly stable in combination with aspirin.