Using \atop
is abusing its functionality; if you want to turn a screw, sometimes a knife can help, but a screwdriver is surely better.
In other words, use \substack
that has been specifically defined for this task and can accommodate any number of lines. It's also easier to use even for two lines.
\documentclass{article}
\usepackage{amsmath}
\begin{document}
\[
\sum_{1\le i\le n\atop i\ne j}\quad
\sum_{\scriptstyle 1\le i\le n\atop\scriptstyle i\ne j}\quad
\sum_{\substack{1\le i\le n\\ i\ne j}}
\]
\end{document}

The first is wrong; the second is complicated to write. With \substack
you also avoid the warning
Package amsmath Warning: Foreign command \atop;
(amsmath) \frac or \genfrac should be used instead
(amsmath) on input line 6.
\over
(which shares many similarities with\atop
) shouldn't be used in LaTeX documents -- any why\frac
should be used instead. The syntax of the TeX "primitive" commands\atop
and\over
is quite different from that used by most other TeX macros, and if you violate one of these syntax rules you're liable to get weird, bad crashes. In contrast,\substack
is crafted much more robustly.