Some points I'd like to make:
1) In the U.S. as a GA pilot you only HAVE to file if you are going to be IFR. You MAY file if you are VFR, and you MAY use services if you are VFR at any time, UNLESS you are in controlled airspace that dictates contact with Center. Controlled air space is Class A, B, C, or D. Note you only have to Activate (a different process) when you are flying IFR. I routinely use services or file IFR because I fly in a congested area. It's just safer. A buddy of mine who flies out of a different location NEVER uses services, but he's in a pretty open area. I don't know for sure but I would venture that most GA flights on a given day have no flight plan or use no active en-route services.
(As an aside, most corporate aircraft will file since they will be in the Flight Levels (18K minimum) which is Class A airspace. You must file IFR if you are entering Class A.)
2) The privacy issue has much less to do with routes and flying that with the information available immediately to anyone in the world. As a GA pilot and plane owner, you already have my personnel information (address, phone number, business, etc) available to you if you have my "N" number. This is provided by the FAA in a standard database and is considered public record. Tying that to routes I'm flying in my opinion exceeds the standards of the "need to know" and may put my family or myself at risk. I see no reason for the U.S. Government to provide this data to ANYONE in the world to have ANONYMOUS access to gratis (paid for by the U.S. taxpayer) for private aircraft. Especially given the same Government screens out any U.S. Government travel for reason's of privacy and security. Just doesn't pass the common sense test, and it actually costs us money to provide it.
3) People drive down the public roads everyday, and no one tracks them...YET. Since GM and "On Star" is now owned by the Federal Government perhaps that will change. Don't get me wrong, I don't believe in the EVIL Federal Government (I work for the Gov't) , but someone in some agency or department somewhere, for the best of reasons (managing Hurricane evacuation routes?), will point out the benefits of tracking individual vehicles down the road and there's where it will start. It's the slow insidious erosion of basic freedoms, all for the best of intentions, that's the biggest threat to our Republic and our citizenry. Okay, little soap box there, but you get the point. We'll be able to keep an eye on all the members of this forum and their various nefarious dealings ("Running to the 7-11 for Chips Ahoy again are we??").
So I humbly suggest all you guys and gals who think this is just a GA deal pay attention. Finally, it is perfectly acceptable for the citizenry to demand to know "WHY" when a department arbitrarily makes a decision. There are some issues that should be addressed on principle alone, with no regard to consequences, positive or negative. I believe this issue comes close to meeting that standard. I don't beleive the FAA has yet been able to answer the "WHY" satisfactorily.