You could set the Header Line Count to 0, then send the flowfiles to a RouteOnAttribute processor where you can "skip" the first line by routing on the following Expression Language statement:

${fragment.index:gt(0)}

The first line will be routed to "unmatched" and the rest to "matched" or the user-defined property name (depending on the value of the Routing Strategy property). Note that this requires the Line Split Count property be set to 1 in SplitText.

Alternatively, if you are using (or can upgrade to) NiFi 1.3.0, you can use a record-aware processor with a CSVReader. This reader can be configured to (among other things) skip the header line. The record-aware processors also offer better performance when working with flow files that contain many "records" (such as a CSV file where each "record" is a row).