fread is for stream unformatted files; you have formatted delimited file--
If you really only want/need the two columns sotoo (air-code, untested)
ought to do unless the third column is indeed a comma-for-a-decimal point as well as a comma-delimited file. In that case you've got a problem. You'll have to read three values instead of just two or preprocess the file or otherwise handle the decimal separator as Matlab can't (and you can't expect it to) know the difference between comma-delimiters and decimal places.