A DC9 CREW TAXIED PAST THE HOLD SHORT LINE DURING TAXI FOR TKOF AT ROC.

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IT WAS THE LAST LEG OF A 5-LEG DAY. DUTY TIME WAS AT XA30. NIGHT TIME. ALSO LAST LEG OF A 4-DAY TRIP. GND ATC GAVE INSTRUCTIONS TO; 'TAXI TO RWY 22 VIA TXWY C; TXWY D; HOLD SHORT OF RWY 28.' THE CLRNC WAS READ BACK APPROPRIATELY. CONSTRUCTION IS UNDER WAY AT THE ROC ARPT. THE RWY THRESHOLD IS DISPLACED AND THE ONLY ACCESS TO RWY 22 IS VIA RWY 28. AT THE HOLD SHORT LINES OF RWY 28 ON TXWY D WE HELD SHORT. AT THAT TIME THERE WERE 2 ACFT WAITING FOR TKOF. THEY WERE POSITIONED ON RWY 28. THEY WERE AN A320 AND A CRJ. WE ASSUMED WE WERE IN LINE FOR TKOF. WHEN THE PREVIOUS ACFT DEPARTED; WE FOLLOWED IN LINE DISREGARDING THE HOLD SHORT INSTRUCTION. WHILE WE MISSED THE HOLD SHORT INSTRUCTION; WE DID NOT DO IT OUT OF LOSS OF POSITIONAL AWARENESS ON THE ARPT. WE DID NOT TAXI ONTO AN ACTIVE RWY WITH LNDG OR DEPARTING TFC. AFTER THE CRJ DEPARTED WE ASKED FOR TKOF CLRNC. TWR INQUIRED AS TO OUR POS. WE WERE ON RWY 28 SHORT OF RWY 22. WE THEN RECEIVED CLRNC FOR TKOF. THE CTLRS WERE CLR WITH THE INSTRUCTIONS; HOWEVER; THE ASSUMPTION OF BEING ON RWY 28 WAS OUR FAULT. SUGGESTIONS TO IMPROVE THIS SIT: STAY ALERT AND DON'T ASSUME. ALSO; AVOIDING TAXIING ACFT TO RWYS VIA ACTIVE RWYS; ESPECIALLY IF SEVERAL ACFT USE THEM.