I can see the source of your confusion: If you use Head[f[x]] and Head[5] you get f and Integer respectively. Then, you read the documentation
Apply[f,expr] or f@@expr replaces the head of expr by f.
and you expect Cos@@5 to replace the Integer head by Cos. The way I explain it to myself is by saying Mathematica has two (types of) heads ;-) One type is for expressions such as f[x] and the other is for expressions such as 5. I even have names for them: explicit and implicit heads. Then I conclude: Apply replaces explicit heads only.
Now, in {1,2}, the head is an explicit one. Thus, Plus@@{1,2}=Plus@@List[1,2]=Plus[1,2]=3.
The @ symbol is easier to understand. f@x is just f[x]. So, Plus@{1,2}=Plus[List[1,2]] and the result is List[1,2] because you are not adding anything to List[1,2]. If you want to add something to List[1,2], it must be included as another parameter to Plus. Try Plus[List[1,2],a].
As mentioned in the comments, the documentation does not warn about these two types of heads. If you look closely, you will find a warning in Possible Issues in Apply and in the 3rd statement within details in AtomQ. I would have expected some clarification in Everything Is an Expression. A naive reading of it suggests that 5 and Integer[5] are the same thing.
@@is described at length in the documentation forApply.@is harder to find in the documentation: seePrefix, – Michael E2 Nov 14 '13 at 20:03?FunctionName. But when you do type in?@you get nothing useful, likewise for@@. So my next step is usually a web search, but "at symbol mathematica" doesn't really return any useful results in Google either. – Jason B. Nov 14 '13 at 20:07?@@inside a notebook, that is not what I get as the output. To find that, I have to specifically open up the documentation center from the Help menu and type it into the search box. – Jason B. Nov 14 '13 at 20:22Prefixis confusing. The inputf@xis processed to be equivalent tof[x], and is not the same asPrefix. The@sign as input is interpreted by syntax rules; I don't think it is translated as a real function. I realize on rereading what I wrote above is rather misleading! This is a better reference: http://reference.wolfram.com/mathematica/tutorial/SpecialWaysToInputExpressions.html – Michael E2 Nov 14 '13 at 21:56@@and execute the menu command Help > Find Selected Function (cmd-shift-F on a Mac or F1 on Windows) you get a link to the page for Apply respectively. For@, you get a link toPrefix, which is not what is wanted. This has been mentioned before on this site, but I can't find where. – Michael E2 Nov 14 '13 at 22:00Prefixis not the same as@and the latter remains nameless. – DavidC Nov 14 '13 at 22:09