Even if you have changed to Google Chrome your default browser in Linux, Thunderbird will not respect it. It will continue to open links in Firefox.
Under Linux (Ubuntu and its derivatives for sure) there is only one way to amend this. Go to .mozilla-thunderbird, find the directory for your profile (something like rv7dwavi.default) and open the file prefs.js.
Then search for the strings network.protocol-handler.app.http and network.protocol-handler.app.https.
Usually these directives are missing so you can safely add them anew as follows:
user_pref("network.protocol-handler.app.http", "google-chrome");
user_pref("network.protocol-handler.app.https", "google-chrome");
That's all and from now on Thunderbird will open all links in Google Chrome.