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Are there any issues that I should considered by not putting the physical directory of my websites under inetpub/wwwroot?

I'm placing them under inetpub/ftproot.

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You should consider having proper permission on the desired folder when using a different folder other that inetpub\wwwroot. Please make sure you check the article Default permissions and user rights for IIS 6.0 if you are using IIS 6.0

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it's actually IIS 7 – seanlinmt Mar 16 '10 at 6:06
doesn't matter.. until you have good permission configured on the Web site root folder. – Vivek Kumbhar Mar 16 '10 at 15:02

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