On what basis might Bobby Rupp have been considered a principal suspect in the Clutter case?

Herb Clutter disapproves of the relationship: while the Clutters are Methodist, the Rupps are Catholic, and for this reason he will not consider allowing Nancy to marry Bobby. Nonetheless, Herb is cordial to Bobby.

Also, Bobby Rupp was the last to see them alive which immediately casts suspicion on him. This is somewhat alleviated by Nancy's diary entry from that night which says "Bobby left at 11:00". Obviously, Nancy was alive when Bobby left that fateful night.