Clive Strong notes that an index rebuild will reset certain DMV counters:
As it transpires, an index rebuild will reset the counters for this index within the sys.dm_db_index_usage DMV and this is potentially very dangerous unless you are aware of this. Normally, we determine whether or not an index is in use by looking at this information, but if you perform regular maintenance on this table, you could be resetting the data which you rely on for an accurate decision.
Read the whole thing.