The Belgians were primarily afraid that if they rolled over and let the Germans move through the country, that they would never leave. You have to consider that a field army contains a lot more than just the frontline combat troops. Supply depots, security forces, headquarters, hospitals, and all kinds of troops are required to support an army on the move. While the Germans were busy fighting in France, their rear support services would have been setting up shop across Belgium. Had they been victorious, the Belgians feared that those troops would have never left, and at that point there would be little they could do to remove the German army. By resisting in 1914, even though successful defense was always unlikely, the Belgians put themselves on the Allied side, and drew common cause with England and France. The issue of Belgian neutrality was small for the French and English, who had already agreed to fight together. However, for the Belgians it meant that the Allies had to save Belgium to declare complete victory.

So in effect, siding with the Allies gave the Belgians the possibility of independence, while siding with the Germans held nothing but occupation and eventual annexation.