In ST: Into Darkness the Enterprise flew straight to Qo'nos without a problem as it seems.
How is that possible especially if the Klingons posed a real threat to the Federation?
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They did not:
MARCUS: As part of our defensive strategy, 31 developed a new photon torpedo. (calls up hologram) Long range and untraceable, it would be invisible to Klingon sensors. I don't want you hurt, but I want to take him out. You park on the edge of the Neutral Zone, you lock onto Harrison's position, you fire, you kill him and you haul ass.
So the intention was to park on the edge of the neutral zona and use the torpedoes (which are long range) to reach Qo'nos.
Once they decide to change the plan the use a contraband cargo ship to get to Qo'nos. The Enterprise never makes it into Klingon space.
SULU [OC]: Please have the trade ship we confiscated during the Mudd incident last month fuelled and flight ready. Captain Kirk is en route to you now.
SPOCK: Ready to deploy, Captain.
KIRK: Lieutenants, lose the red shirts. You are K'normian arms dealers. Put those on.
As far as Kirk and the crew knew at that point in the movie, no ship was capable of catching Enterprise while Enterprise was travelling at warp(1). They only considered opposition to be a possibility for the cargo ship's sublight travel to and from Qo'noS, and for the team's brief time on the planet's surface. For the vulnerable stage of the mission, they relied on speed, stealth, and subterfuge --- and were promptly caught.
(1) Inferred from a later scene, when Enterprise is on the run from Vengeance:
CAROL: He's gonna catch up with us, and when he does, the only thing that's going to stop him destroying this ship is me, so you have to let me talk to him.
KIRK: Carol, we're at warp. He can't catch up with us.
CAROL: Yes, he can. He's been developing a ship that has advanced warp capabilities, and I
SULU: Captain! I'm getting a reading I don't understand.
(Vengeance is chasing Enterprise through the slipstream, sorry, warp space. Weapons are fired, causing a hull breach in Enterprise's starboard side. Then the nacelles are hit and Enterprise drops out of warp.)
Transcript: Star Trek Into Darkness (2013)