<p>Every time I publish the application in <a href="http://en.wikipedia.org/wiki/ClickOnce" rel="nofollow noreferrer">ClickOnce</a> I get get it to update the revision number by one. Is there a way to get this change automatically to change the version number in AssemblyInfo.cs file (all our error reporting looks at the Assembly Version)?</p>

You'll probably need to create a piece of code that updates AssemblyInfo.cs according to the version number stored in the .csproj file. (The ClickOnce deploy version is stored inside an XML tag.)
You'd then change your .csproj file to run this bit of code when Publish|Release build is performed. The MSBuild folks have blogged about how to perform custom actions during certain build types; check the
MSBuild team blog
.