Edit : I found an exact duplicate of your question :here. It seems to be an issue with iTerm not supporting 256 colors by default.
The usual problem with color scheme and terminal is that terminal are often limited to 256 colors, and GUI color scheme are using 2^32 colors. So some of them are not correctly rendered in terminal.
There is a simple test to check: if you are lauching the GUI version is the color scheme rendered correctly ?
The possible solution are :
1. Convert your color scheme to 256 colors using the following plugin : CSApprox.vim
2. Choose a different color scheme. (Often on Vim.org color schemes compatible with Terminal have "256" in their name, like "wombat256" for example)
3. Use a GUI version like MacVim or GVim
If I remember correctly, the color sheme Zenburn is working nicely with both GUI and terminal version. It is rather dark with pastel colors.
Personal story : after spending ages to fiddle with color scheme to get something right for terminal, I switched to the GUI version. The GUI version with the icon bar hidden is not really different to terminal version anyway, as long as you are working locally