so....you have set the html tag <code> to have the font...but you don't have any <code> tags in the epub you posted.
Your src reference needs to be the exact same as your epub...capitalization matters.... so, as Foozle mentioned, /fonts/ is not the same as /Fonts/. I used Sigil menu 'Tools/Restructure Epub to Sigil Norm" - although that isn't strictly necessary, it makes the structure and naming of the ePub something I can rely on - and am familiar with.
In this case, I cleaned up some of the duplicate css and moved the font to the header tags.
Code:
@font-face {
font-family:'Chomsky';
font-weight:normal;
font-style:normal;
src:url('../Fonts/Chomsky.otf')
}
body{margin:5%; text-align:justify; font-size:medium; background-color:#FCF5E5}
h1,h2,h3,h4,h5,h6{font-family:"Chomsky"; text-align:left}
nav#toc ol,nav#landmarks ol{padding:0; margin-left:1em}
nav#toc ol li,nav#landmarks ol li{list-style-type:none; margin:0; padding:0}
a.footnote-ref{vertical-align:super}
em{font-style:italic}
em em{font-style:normal}
code{white-space:pre-wrap}
span.smallcaps{font-variant:small-caps}
span.underline{text-decoration:underline}
q{quotes:"“" "”" "‘" "’"}
div.column{display:inline-block; vertical-align:top; width:50%}
div.hanging-indent{margin-left:1.5em; text-indent:-1.5em}