The ifthen package cannot evaluate expressions like \i/3 or int(\i/3) in a condition. You have to compute the integer expression first and then compare strings. You can use \numexpr and \number:
\documentclass[border=25pt]{standalone}
\usepackage{tikz,ifthen}
\begin{document}
\begin{tikzpicture}
\foreach \i in {1,...,12}{%
\ifthenelse{\equal{\number\i}{\number\numexpr\i/3*3\relax}}%
{\draw[purple] (.75*\i,0) node {\i};}%
{\draw[blue] (.75*\i,0) node {\i};}%
}
\end{tikzpicture}
\end{document}
Here \numexpr\i/3*3\relax computes (\i/3)*3 with integer division,
and if it is equal to \i, then \i is divisible by 3.

Note that for this kind of task it is generally better to avoid ifthen altogether and use primitive numeric conditionals such as \ifnum instead. For example:
\documentclass[border=25pt]{standalone}
\usepackage{tikz}
\begin{document}
\begin{tikzpicture}
\foreach \i in {1,...,12}{
% compute \rest = \i mod 3
\pgfmathtruncatemacro{\rest}{mod(\i,3)}
\ifnum\rest=0
\draw[purple] (.75*\i,0) node {\i};
\else
\draw[blue] (.75*\i,0) node {\i};
\fi
}
\end{tikzpicture}
\end{document}