Kendra Little reports that rebuilding an index no longer clears out sys.dm_db_index_usage_stats:
Testing SQL Server 2016 RC0 today, I see that the bug for index_usage_stats has been fixed in this release! When I generate scans, seeks, and updates against an index, running ALTER INDEX REBUILD no longer resets the information. I can still tell which indexes have been used and which have not since the database came online, just like we had in SQL Server 2008 R2 and prior.
Kendra has created a Connect item to fix a separate bug where rebuilding an index clears out the missing index recommendations for that table.