ALTER INDEX is a DDL operation, therefore it will be making changes to the system tables, hence needing locks on the rows in the underlying metadata. Without seeing the deadlock graph, that's about all I can guess.
A select will always be chosen the victim in a deadlock by default, as it has done no work that needs to be rolled back.
Gail Shaw
Microsoft Certified Master: SQL Server, MVP, M.Sc (Comp Sci)
SQL In The Wild: Discussions on DB performance with occasional diversions into recoverability