How can I set site.com/node/1 into site.com (clean)?
I think @JimmyKo and @Gulok, misunderstood the question OR I myself misunderstood the question(If so comment me I will delete the answer).

As stated in the question,


  I am trying to get my site as site.com and when I type the URL, I get
  site.com/node/1.


The issue is user want site.com as his Front-Page but when he types site.com he is redirected to site.com/node/1.

If this is the case. You need to set your home page. Now to set the home page, you need to go Configuration/Site information for D7 and Configuration/Basic site setting for D8, there you set the front page path as shown in following images.

For D7 case,


  


For D8 case,


  



Now Reverse Case, In case I misunderstood the question

If you want to make your front page to some node like node/1, Go the same path as mentioned above and put your path there as shown in follwoign image. NOTE: There is a difference between D7 and D8 path which is '/', you can see in following images.

For D7 case,


  


For D8 case,


  



Other case(Less likely): Have downloaded other Font-page creating module or are you using panel which provides the option of making any panel a front-page. If that is the case, those modules are overriding this default setting, Hence you have to modify accordingly.