Gustav is correct. Editing the file /usr/bin/xdg-settings as described
in the bug report has fixed the problem for me in 15.10. Perhaps this
will help someone at least eliminate the annoyance for now.

The offending line for me is line #198
command="`grep -E "^Exec(\[[^]=]*])?=" "$file" | cut -d= -f 2- | sed -e 's/ 
.*$//'`"

rectified to:
command="`grep -E "^Exec(\[[^]=]*])?=" "$file" | cut -d= -f 2- | sed -e 's/ 
.*$//' | head -n 1`" 

After making this change, you can set the default browser within the
Chrome settings as Nikita mentioned, and it will succeed.

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You received this bug notification because you are a member of Desktop
Packages, which is subscribed to xdg-utils in Ubuntu.
https://bugs.launchpad.net/bugs/1509139

Title:
  Shows "Chromium isn't your default browser" since 15.10.

Status in Chromium Browser:
  New
Status in chromium-browser package in Ubuntu:
  Confirmed
Status in google-chrome package in Ubuntu:
  Confirmed
Status in xdg-utils package in Ubuntu:
  Confirmed

Bug description:
  Since the 15.10.  upgrade Chromium shows on every launch "Chromium
  isn't your default browser", even when i select "Set as default" or
  "Don't ask again".

  Chromium is set as default application for "Web" at System Settings ->
  Details -> Default Applications.

  Version 45.0.2454.101 Ubuntu 15.10 (64-bit)

To manage notifications about this bug go to:
https://bugs.launchpad.net/chromium-browser/+bug/1509139/+subscriptions

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