In LyX, how can I make the pages numbers start from the second page? (i.e., making the first page, which is the table of contents in my case, not having a page number on it)
Since LyX (up to recent version 2.0.x) only supports globally changing the pagestyle (in "Document > Setting... > Page Layout") using TeX code/ERT is a workaround.
If the first page should not be numbered then insert the TeX code/ERT
at the beginning of your document (before the table of contents(TOC)). This will clear the page number of that page (see also http://tex.stackexchange.com/a/44153).
(To suppress page numbers for the whole TOC
If the page numbers should be reset at some point, you can add the TeX code
on a (new) page / after a page break.