Constitutional rights

I read a thread today on my favorite backyard chickens forum (backyardchickens.com) that this veteran in Bethlehem, Pennsylvania got some chickens that help him deal with having Post Traumatic Stress Disorder.  His idiot neighbor protested him having them because his coop was 4 inches too close to the property line.  Give me a break!  4 inches?!?!  Here vets are coming home from these damn wars going on over in no man's land, and they are messed up to the nth degree.  One of them finds comfort and peace from all the baggage they are left to deal with by keeping a few chickens, and his dumb ass neighbor has the balls to complain about it????  I apologize for the language, but really????
So, a fellow veteran and his wife hear about this and build him a chicken tractor (portable coop to you non-chicken folks) and now he can keep his chickens.  Thank Goodness!  Isn't that just awesome that someone would do that for him?
I am confused, I understand why we have laws regulating the keeping of animals in towns.  But I don't understand the restriction of keeping chickens in your backyard within a reasonable number, of course.  What happened to our Constitutional right of pursuit of happiness?  To some people like this one vet, it is truly about the pursuit of happiness.  It seems like more an more the government is taking away the rights of people to actually pursue happiness.  There are extremely stringent laws on how dairy products are handled for raw sale and consumption, like just because we don't want to go cook I mean, pasteurize all the goodness out of our milk to then fortify it to return the goodness back into it that was there naturally in the first place that was killed in the heating process, that raw milk is all bad and carries e-coli.  There was a farmer who was selling raw dairy to consumers here in my own state, who was blamed as part of a small e-coli outbreak because someone he sold to got e-coli.  Uh, there were other people in that same outbreak who had never had any of his products, so how can it be his fault?  I am confused.  So, something like that comes up and the first people to get blamed are the ones doing it raw or natural or organically.  That is proposterous!  The fact is, that our food that we buy in our grocery stores is mostly shipped from over 1,000 miles away at a minimum, and it isn't all that fresh either.  SO, isn't it just possible that the really bad food stuffs are not from the local farmer trying to sell good, wholesome (key work WHOLE) and fresh foods is the one to maybe NOT worry so much about.  But, oh yeah, the neighbor selling the raw milk isn't to one lining the pockets of the lobbyists so that bills can get passed to help out those big guys who cook the milk and spray our fruits and veggies so they can ship them across continents and across the country, so they can arrive in our grocery stores nice and fresh(?).
I know, how did I go from a rant about chickens to this?  Well, it all goes together.  This is getting insane.  Like someone has to legislate what we can and cannot buy to eat because we are too stupid to decide what is good for us?  Is that what this is about?  I don't think so.  I think it is more about  money and the little people trying to do what is good and what is good for us trying to eek out a living by doing so, getting in the way of big food corporations that won't stand for some little guy getting in their way of monopolizing the supply of food. 
What is next?  Am I going to be breaking the law if I plant my own vegetable garden?  Are my chickens going to be taken away?  What?  I don't understand how the lawmakers use the Constitution to tell us what we can and cannot do, but they blatantly disregard the rights that same document gives each and every one of us to make our own choices.
It just doesn't seem right.