I don't think it is as dark as you see it. I tend to search Google and do part of my research (for work) more and more from a TOR browser. Not because I do anything wrong, just because I don't want every search to be registered with my Google account (and who knows who else's cookies are in there anyway).
The other thing is: if every household would run a full TOR node (not exit, just run TOR or i2P all the time), it would also make traffic a lot less suspicious.
For Average Joe: call it "TBP secure browser"
To a certain degree I agree with you though: people hear "darknet" and they think you are doing something wrong. Maybe people who understand the idea and the tech behind could do a little better to make them understand, that it is not just illegal stuff there, it is also a tool not to expose them 24/7 to surveillance... I don't even mean NSA, I mean Google/Facebook/Yahoo/MS and their advertisers and the data miners who allow companies to look up your arse 24/7.
And again: I don't mind Facebook showing me a shoe ad because I searched "Mountain bike shoes" on Amazon. However, I would mind a company not giving me a contract because I searched "drone hacking" on Google.... because they won't understand the difference between "hacking a military drone" or "hacking a $200 quad-rotor to have decent RC control instead of the iphone wifi"
That search attached to your profile would also make any TSA inspector crawl up in your butt in no time too
Could continue the stupid examples all day to demonstrate how something harmless could turn against you because everything is logged and attached to your accounts instantly, but it is not you I have to convince, it is Average Joe who should be made aware of these.