The government might read my WhatsApp messages - so what? They have been able to listen to my phone calls for ages. If there's something I want to keep private (and there is - it's not like "I have nothing to hide"), I will simply not use WhatsApp or any other communication channel I don't fully trust.
I don't care as long as the owner of the coffee shop I'm currently I cannot read my messages.
I think the problem is that security is an ongoing conversation between the government and the people. My guess is that most people, if pushed to a firm position, would probably agree with:
a) The government should have the right to look at communication to stop bad things.
b) The government should have to individually prove before an independent court that any one use of that power is justified.
The difficulty is that the government unilaterally broke (b) by having a rubberstamp court and a policy that let them collect everything and choose when to look at it.
And the response to the government's action is to start looking to redress this privately. I.e. a market solution to a perceived deficit of privacy. I suspect that if they had kept (b) intact, there would be much less call for absolute security, and much less of a solid argument for it.
For instance, something that really gets on my nerves is when I search for something on amazon and when I am reading a blog post about something completely unrelated to my amazon search, I see an advert related to my search.
This is just really annoying, its not like I want to hide the fact I am looking for a new TV its just that its really annoying and its an invasion of my privacy. Its just like having a helpful but nosy neighbor who gets the mail for you.
Also, just like you said, if someone has something to hide they will find alternatives to hide it, but why inconvenience us, the law abiding citizens, why invade whats our own business?