Why did Honda only provide a screwdriver for the 2009 Rebel 250 tool compartment?

That's right. A screwdriver. For a motorcycle. For "maintenance."

To answer the question in the headline: cost savings. More specifically, the screwdriver is made available so that the left side cover could be opened to reveal the user manual in a plastic window. 

To access the compartment, stick your key into the finicky plastic hole and turn right. Be firm but don't be harsh with the turn. The plastic will feel sticky. Once you have it turned, slide and pull the cover off left, down, and out. 

I feel frustrated because this compartment is difficult to open, made out of plastic, has very little space to work with, and doesn't really offer enough space for tools needed in emergencies. Time to stock up with more tools.