In an economy where there are more job seekers than jobs....you are easily replaced. You're a dime a dozen. Your just another guy with a college degree looking for a job. Apparently your "school" that taught you to negotiate did not teach you to look at the big picture and see if you were in a power position.
You weren't.
As you have learned, in corporate America, when you apply for a job - unless you are applying for a position where there are lots of jobs and very few people with the skills to do them - you're not going to be able to negotate much other than salary. And with no experience, there is no room to negotiate this either.
Vacation time - is a standard policy for all employees. You don't get to be special.
Telecommuting - unless this is offered to other employees - you don't get to be special.
Regarding your salary demand - your "research" (websites) is half baked and lazy. I can look my job up on web sites and the salary is wrong. Zillow also has my house value wrong too.
If you want to know what the salary range is for a job you are applying for - then you work the phones and you get off your computer and meet people. You talk to live human beings and find out what the salary is in your area for that job.
Addittionally, the company knows what their competitors are paying. They know what the job is worth for someone with little to no experience. I bet their starting pay is competitive to what other companies are paying for the same job.
If you think you deserve more money than what they are offering, then you negotate based on what you bring to the table. What skills, background, education, experiences do you have that another candidate does not that makes you worth more? If the answer is "none" then starting salary is just what you deserve.
In essense "but that's not what others are getting paid" does not entitle you to more money. Just like, "but Billy's mom lets him do it" did not persuade your parents to let you do things you wanted to do. They don't care what others are doing. They offered what the job is worth to them. If you don't have any special skills, education, experience etc that make you worth more then you're not worth more.
Your internship is why they pulled your resume out of the stack of 200 and called you. That relationship is why they offered the job to you. That's why you were their first choice.
That job was yours and You blew it. They've offered the job to their second choice who was very happy to take it.
At this point, all you can do is learn from it. Next time you get a job offer, just accept it.