newscaster, I can't see why the Egyptian authorities would say no considering the UK-Egypt bi-lateral is quite liberal. SD and for a short time IY were granted rights on the CAI-LHR route.
Besides MS already operate
-CAI-LHR
-LXR-LHR
-SSH-LHR
and BA (thru partners too)
-CAI-LHR
-HBE-(BEY)-LHR (no traffic rights on BEY-HBE sector)
....and soon
-SSH-LGW
-HRG-LGW
Also bear in mind Astraeus have scheduled flights between the two countires
LGW-SSH (3x weekly B752)
MAN-SSH (1x weekly B73G)
As for Philippine Airlines applying to serve MNL-RUH-CAI that was only a rumour. If indeed that was true it was probably refused because PAL wanted traffic rights on the RUH-CAI sector which the Egyptian authorities would not grant to protect Egyptair (the Middle East is MS's most profitable market).
-AF currently fly CDG-CAI-RUH with no rights between CAI-RUH
-KE currently fly ICN-DXB-CAI with no rights between DXB-CAI
-LH will start FRA-CAI-DMM flights this October with no traffic rights between CAI-DMM.
The only exception is SQ who fly SIN-DXB-CAI with full passenger traffic rights between DXB and CAI.
The Egyptian authorities are quite protective of Egyptair (as it is a government owned airline) so they try to minimise any other airline competing against it besides the official carrier from the destination country. Unfortunately this also has a negative effect on private Egyptian airlines, as all 9 of them are restricted to the charter market so not to 'step on the toes' of Egyptair.
There has been talk that authorities would become more lenient (and it has changed slightly) but it might take time before the Egyptian market is truely liberalised.