R source code in rmarkdown HTML output is placed between a <code> tag that lives inside a <pre> with class r. You want to apply the style to all instances of <code> that don't share this property. Here's an example using the :not() selector:
pre:not(.r) code {
font: 12px Monaco, "Courier New";
color: red;
}
For bookdown output formats you want to exlcude instances of <code> with class sourceCode:
code:not(.sourceCode) {
font: 12px Monaco, "Courier New" !important;
color: red !important;
}
Note that the use of !important is required here because the default styles have precedence.