How to change footnote number to non-superscript

I suppose that, in the main text you still want a superscripted footnote mark.

Here's a patch to \@makefntext which does the trick. I didn't try to check if there are any side effects. Note I slightly changed some of your lengths settings, to suit my personal taste.

\documentclass[11pt,oneside]{book}
\usepackage[letterpaper]{geometry}

\usepackage{setspace}

\renewcommand{\footnotesize}{\small} % 10pt footnotes in 11pt doc instead of 9pt

\usepackage[hang, flushmargin,splitrule,multiple]{footmisc}
\usepackage{etoolbox}

\makeatletter%%
\patchcmd{\@makefntext}{%
\ifFN@hangfoot
\bgroup}%
{%
\ifFN@hangfoot
\bgroup\def\@makefnmark{\rlap{\normalfont\@thefnmark.}}}{}{}%
% %%%
\patchcmd{\@makefntext}{%
\ifdim\footnotemargin>\z@
\hb@xt@ \footnotemargin{\hss\@makefnmark}}%
{%
\ifdim\footnotemargin>\z@
\hb@xt@ \footnotemargin{\@makefnmark\hss}}{}{}%
\makeatother

\setlength{\footnotemargin}{1.25em} % Between marker and text
\setlength{\skip\footins}{1\baselineskip} % Between main text and note rule
\setlength{\footnotesep}{\skip\footins} % Between footnotes [= previous]

\renewcommand{\hangfootparskip}{0pt}
\renewcommand{\hangfootparindent}{1em}

\doublespacing
\parskip=0pt

\usepackage{lipsum}

\begin{document}

Lorem ipsum...\footnote{Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Ut purus elit, vestibulum ut, placerat ac, adipiscing vitae, felis.

Curabitur dictum gravida mauris. Nam arcu libero, nonummy eget, consectetuer id, vulputate a, magna. Donec vehicula augue eu neque. Pellentesque habitant morbi tristique senectus et netus et malesuada fames ac turpis egestas. Mauris ut leo. Cras viverra metus rhoncus sem. Nulla et lectus vestibulum urna fringilla ultrices. Phasellus eu tellus sit amet tortor gravida placerat. }

\end{document}