Small Signal BJT Model
From the model viewpoint, the voltage-controlled current source is pointing in the direction that an increase in input voltage leads to a decrease in output voltage. 

From a practical point of view, more voltage on the base means more collector current, which decreases the output (collector) voltage in an NPN common-emitter configuration. 

If your output was taken across the load resistor (from Vcc to collector) rather than from the collector to ground, then the sign would be positive.