Eric--I think the short answer here is that you really need a lawyer to take you through this. (I'm saying that up front, because the rest of this answer is going to be really long and is likely to further muddy the waters....)
A few years ago, I was involved in setting up an international trade association hq'd in Michigan, but it wanted chapters set up throughout the US and the rest of the world. I can certainly understand your confusion--I know the options made my head spin!
Trying to keep this relatively short, I can tell you a few things I learned; maybe this will help you sort things out.
Tax exemption is first a Federal/IRS issue (and it is NOT the same as being a nonprofit). No matter where you set up your corporate hq, you'll need to file for tax exemption with the IRS. After that, any chapters you set up, even if they are separate corporations (and they don't have to be) will likely fall under that umbrella; you'll have to file for a group exemption with the IRS at that point. Most states (if not all; I'm not sure) then will grant exemption from income taxes based on the Federal exemption. But, you're not necessarily exempt from sales taxes at the state/local level--every state is different, and if you don't have a physical presence in each of these states, I could not even begin to guess how that might impact you.
Setting up your corporation as a "nonprofit" is a state by state issue.
(Not all states even use the term "nonprofit." Here in VA, they will tell you there is no such thing as a nonprofit corporation, only "nonstock" corporations.) You need to investigate a whole bunch of stuff to figure out which arrangement is most advantageous. The main corporation does not even need to be set up in MD; you could incorporate in Delaware (there's a reason there are so many companies incorporated in DE; has to do with filing fees and ease/speed of incorporation) if you wanted to. You need to look at not only the filing fees involved in each state, but whatever other requirements they have for corporations that might be important to you. For example, many state laws dictate certain minimums for meeting quorums, or frequency of annual meetings. If you are physically located in one state, but incorporated in another, you are called a "foreign" corporation in the state in which you are located. So you need to compare the domestic (=> you're located in the state in which you incorporate) versus foreign corporation annual filing fees. You also need to look at fees for a "registered agent" located in all the different states in which you incorporate, if you decide to incorporate each chapter (and again, you don't have to do that).
That's just some of the stuff I can come up with off the top of my head. I don't recall MD's laws being particularly onerous; your best bet is probably just to go ahead and incorporate in MD for now and deal with the rest later. (But keep in mind how much you paid for this advice!
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A corporate lawyer who deals with this kind of stuff all the time can sift through this many times faster than you--they have resources to all kinds of filing fee information, etc. that you can't easily get to. I remember from another post that you had a lawyer willing to help you; you should probably take advantage of that. But, the virtual component of your organization puts a twist on this whole thing that he/she may not have the expertise to deal with---I'd just make sure the person knows the limitations of their knowledge and is willing to get more expert help if they need it.
Finally, I know a DC based lawyer who has an office in Baltimore who might be able to help you (he helped me with the Michigan thing). If you email me, I'll get you that information.
