yEd supports these file formats: http://yed.yworks.com/support/manual/fileformat.html
If you can transform .cap/.pcap files to GraphML (yEd's default file format), you should be fine.
Well, unfortunately converting *.cap/*.pcap into GraphML is quite difficult.
However according to Is there a way to programatically export files using Wireshark's facilities? it is possible to use WireShark (or the command line tool tshark) for exporting *.cap/*.pcap files in an XML format. If you are able to create an XSLT stylesheet for transforming the resulting XML files into GraphML, you may import the XML files exported from WireShark together with your custom XSLT stylesheet into yEd. Creating an appropriate XSLT stylesheet is the difficult part.