The libpcap file format has a field in its global header called network
that specifies the data link type. This corresponds to documentation over at the tcpdump project about various Link-Layer Header Types.
From there, you would be able to determine how many bytes the link layer consists (if any) and will be a sure fire way for you to parse pcap files created with the libpcap library.
I am not aware of a program options in the "libpcap family" that would allow you to just capture starting at the transport layer.