Can I set the format of an entire column except for the header?

Use the array package to specify \itshape for the second column, and use the \multicolumn command to cancel the effect for the header.

\documentclass{article}

\usepackage{array}

\begin{document}

\begin{tabular}{l>{\itshape}ll}
PFT & \multicolumn{1}{l}{Scientific Name} & Common Name\\
PFT1 &  & \\
 & Elymus repens & quackgrass\\
 & Koeleria macrantha & prairie Junegrass\\
 & Elymus canadensis & Canada wildrye\\
\end{tabular}

\end{document}