While I was searching for materials for my research topic, I found a research paper which is signed as copyright by "Some organization". Does that mean that I could not use the content of this paper nor the ideas it presents until the paper owner gives me permissions?
Not necessarily. Copyright prohibits you from presenting the work as yours under any circumstances. In addition, it prohibits you from publishing or recopying large segments of the work, without securing the permission of the owner of the copyright.
However, the existence of copyright does not exclude you from citing the work of others, nor mentioning what their key ideas are. Such use of copyright is covered by fair-use guidelines (archived version). Under these circumstances, though, you are still responsible for following the proper citation procedures of your university or the journal to which you are submitting the work under question. Note, however, that this is a tricky balance, and you should be careful to directly quote only the material you absolutely need to duplicate, as fair use is not an absolute guideline.
The short answer: unless the document is marked "confidential" you can probably quote short passages verbatim and you can certainly make use of the ideas.
To expand on some of the other responses given here: In most jurisdictions, copyright allows the protection of the expression of an idea (e.g. as written down in a book or article) but not the idea itself. Legal protection of ideas is covered by patent law, which is much more restrictive than copyright, with much shorter periods of protection.
It's also worth knowing that phrases like "All rights reserved" are partly redundant these days in most countries – all works are copyrighted automatically, whether or not they include this phrase or similar. However, it's still useful to know who owns the copyright to a particular work.
What is referred to as "Fair Use" under US copyright law may not exist or may be very different in other jurisdictions. For example, in the United Kingdom there is a rather more restrictive version called "Fair Dealing".
If you have some time to kill, Bound by Law is a useful comicbook-style introduction to copyright.