When I export my inDesign document with Hyperlinks to PDF the links all go to the correct places and work absolutely fine. The only problem is that every time you click on one it opens a new browser window with the homepage (google in my case) and another one with the destination URL. It only does this if there is not already a browser window open so clicking on multiple links in the PDF only opens one new window for each URL apart from the first one. When you click on the mailto link it opens my homepage, plus another empty browser window, plus a new email in my email application.
I am working on a Mac in inDesign CS with Acrobat 6.0 Professional and my internet browser is Safari.
I did this on InDesign CS3 on PC and it worked fine using internet explorer.
Then took my pdf and opened it on the mac and it worked fine (Safair was not booted when I clicked on the link).
I looked over the preferences in Safari, and the only one of interest was Open links from application, and mine is set to "In new window". Which doesn't make sense, as when i already had a window open, it did open the pdf link in a new window.
I beleive your problem will not be solved within InDesign or even the mighty Acrobat, but within Safari or somewhere in your Mac OS.
Does this happen if you click on a link in any other application?
Can you try this clicking on the link on another computer?
To confirm, can you try downloading this simple test generated from my computer.