The easiest answer is that you might not have had enough starting material. If you don't have enough DNA in your samples, then you won't get much DNA out. That would be my first suspicion if you followed the protocol correctly. Try again with other samples. Good luck!

I would check the OD of the culture prior to mini prep to make sure it has grown to an expected density. It may be that you have a low amount of DNA to begin with. I typically use 8 mL of culture grown to an OD600 of 1.6-1.8. In addition, from my experience with mini prep some plasmids vectors prep much better than others. For example, using the above starting conditions and same cell lines I typically get 60 ng/uL of plasmid from pET28b vectors but can get 400 ng/uL from pCOLD vectors. Also, make sure you are using an amplification strain such as XL1 Bule or XL10 Gold to grow your culture and not an expression strain such as BL21 (DE3).

If you where expecting a big amount of DNA it might be possible that some of your DNA was not completely released from the column membrane during the elution step.

A possible solution for this would be to elute your DNA with more buffer or water or make a second dilution step. Another problem that i have encounter is that when i load too much sample my DNA yield starts decreasing. If this is your case i´ll recommend loading less sample into your columns.

Hope this helps

Please make sure the plasmid is high copy or low copy. Does the plasmid contain the bacterial toxic gene that can be expressed in E. coli. The bateria may reduce the expression of the plasmid or only low expression bateria can survive. you can increase the amount of E. coli double or triple.