After you export the PDF from InDesign correctly, you need to open the PDF in Acrobat and set the default initial view for that file. This is what controls how the file will display when people open it. They can always change it to their preference, but you can at least pick how the magazine is FIRST displayed.
In Acrobat 9 Pro for Mac, you go to FILE > PROPERTIES and then click on the INITIAL VIEW tab in the dialog box. Set it to your liking and then save the file.
Yep, that works too... if you have acrobat pro and if all (or most, I guess) of your readers are using acrobat reader. but there's a whole bunch of pdf readers out there now and not all of them will honour the acrobat settings (eg. Preview doesn't).
The best thing about that method is it leaves the file as individual pages — making it easier for printing.
It really depends on how you want your reader to interact with the document.