I am also somewhat new around here but I will take a stab at it.
* how I can publish news?
There are two ways to do this: 1) do this in the manager by adding a new document in the news section. or 2) use a front end publishing tool such as NewsPublisher or FDM snippets.
* How can I create different categories?
The easiest way is to place the documents in containers (files with sub-documents) and base the containers on categories. To create a container you can select the container box in the document parameters tab or click on the container and select the "add document here" option which will automatically make the document a container.
* Is it all about creating document hierarchy/tree ? what does it make difference in news and document?
Yes, there is no difference. A news article is the same as a modx document.
* How I can allow my user to submit news?
You will need to use the NewsPublisher or FDM snippets for this for front end users. You can also have Manager users who could do this in the manager.
* How I can have registration and login on my website?
You can restrict pages by applying user/document groups and WebLogin or WebLogin PE snippets to handle the login/out and other user features. Currently MODx has two types of users, Manager and web. Read up on different user types:
http://modxcms.com/web-users-web-groups.html
http://modxcms.com/manager-users-roles-groups.html
The most difficult thing to get a handle on with modX is that there are no ready one stop solutions for stuff, rather there are powerful building blocks that work with very flexible template system that give you great flexibility.
The main snippets that you will need to get a handle on for a news site will be Ditto (for presenting summaries and other preview data, Wayfinder (for navigation based on document tree), Jot (to allow user based comments in posts or articles), WebLogin PE (to control login and user profiles), eform (for processing forms either by email or some other custom method) and either NewsPublisher or FDM for front end news publishing.
For a good look at how Ditto works take a look at the official documentation:
http://ditto.modxcms.com/
To get to grips with Wayfinder check out the parameters:
http://www.muddydogpaws.com/development/wayfinder/parameters.html
FDM is Front-end Document Manager, it is still officially a beta but I find it works well.
http://modxcms.com/forums/index.php/topic,14977.15.html
And lastly, the community here is very helpful so this forum is probably the best resource around for MODx.