If you look under the publication properties, Articles, select the article / table in question and look at the properties of that article you should be able to set "Copy nonclustered indexes" to True and then non-clustered indexes will be copied as part of the snapshot process. That said, if you add an index on the publisher, that will NOT replicate that to the subscriber. That will need to be done manually.
You can also use sp_changearticle to set the schema_option to allow for the copy of nonclustered indexes as part of the snapshot but that is a bit more complex and I would recommend staying in the GUI for this one.
Hope this helps.
“He is no fool who gives what he cannot keep to gain that which he cannot lose” - Jim Elliot