Atom is build on web technologies, so you can use JavaScript and CSS to alter its behaviour. If, for instance, you type "Warning" into a plain-text document and open the Developer Tools, you will see it is rendered as plain HTML:
<span class="text plain">
<span class="meta paragraph text">Warning</span>
</span>
Unfortunately, there are currently no CSS selectors for the text inside a tag-pair, so you would have to create a plugin, or package, in JavaScript/Coffeescript. How to CSS: select element based on inner HTML) provides a good starting point.
Use JavaScript to detect all instances of “Warning” inside the HTML of the editor view, then add a class. You can then use CSS to highlight the line.
Alternatively, you could probably create custom grammar for your log file.