I've got 2 problems with weather indicator in Ubuntu 11.10 with unity.
1) The weather indicator doesn't launch after starting up the system.
2) The icon which is supposed to show clouds or a sun etc. shows a question mark insted.
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For the first problem, just add it to your startup applications. Click the power icon (top right of your screen) and choose 'Startup applications'. Add one with the command
indicator-weather like in the image below.
For the second problem, this is a known intermittent bug with Google. Switch to Yahoo! as the source in the preferences. You right-click on the indicator to access the preferences dialogue.