The EU also publishes detailed statistics that might shed some light on this (Excel file for 2013).
For example, Belgium has a 5.5% refusal rate for its consulate in Moscow. It's still much higher than Estonia's rate (between 0.5% and 0.8%) but the difference is not nearly as dramatic as that between overall acceptance rates. At the same time, Estonia gets virtually all its visa applications from Russia, the Ukraine (which have agreements with the EU) or Belarus whereas Belgium gets quite a few applications from Congo (its former colony) and Morocco. Those consular posts have refusal rates of 30% and more and weight heavily in the overall rate.
It's all anecdotal but I do believe some consulates (including the Belgian one in Congo, which handles most applications for Schengen visas there through the “maison Schengen”) evaluate applications much more skeptically and are prepared to reject them on the tiniest pretense, possibly based on the (perhaps not entirely unfounded) assumption that most Congolese would consider immigrating illegally at the first opportunity.
Also note the very high proportion of multiple-entry visas for Estonia in Russia. This suggests either that Estonia is very generous indeed or that it mostly gets applications from trusted travelers with a regular need to cross the border. Those applicants can get a visa much more easily than people from far-away countries wanting to visit their family for the first time.