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For reading PDFs, the key differentiator is battery life. Also, the aspect ratio of the display on the Kindle is better for reading a document. If the laptop is always plugged in, then the battery life argument goes away. But, reading a document formatted for 8.5 x 11 on a wide screen display is not the ideal experience.

I would also dispute the effectiveness of taking notes on a laptop. As soon as you want to write anything other than text (e.g. diagram or equation), you'll slow to a crawl. (At least, I would slow to a crawl.)

I agree that $500 is a steep up front investment given the similarity in price point to a low end laptop.