TLDR: opportunities of launches to ISS with 6-hour rendezvous are more rare than for 2-days rendezvous.
The main reason of 6-hour rendezvous of Soyuz is to save time for cosmonauts/astronauts to work in ISS. But 6-hour scheme have very tight requirements for ISS orbit. The path of ISS should be exactly above Baikonur cosmodrome at the moment of launch. It occurs not every day. Roskosmos usually makes ajustment of the ISS orbit before Soyuz launch to align them more close. But ISS is big, over 400 tonnes, so only tiny orbit corrections are possible.
As a result - 6-hour rendezvous can't be done at every day. We have to wait for several days usually. For "long" 2-days rendezvous opportunities occur more often. So there is a tradeoff - to wait several days and spend more fuel at ISS orbit correction to launch at fast 6-hour scheme, or to wait several days less to launch at 2-days flight. So, in some cases astronauts can arrive at ISS faster with 2-days scheme.
Also should be noted that upcoming launch of Soyuz TMA-09M have small gap with return of 3 ISS crewmembers on Soyuz MS-07. They landed only 3 days before, but usually the gap between landing of previous crew and lauch of the next was about 2 weeks. So, I think the purpose is to maximise occupation of ISS.
Progress cargo launches also used 6-hour rendezvous. It was done for testing the scheme for Soyuz launches with crew. Now Progress usually take 2-days rendezvous. Short 6-hour trip could have benefits for some sensitive cargo (biological samples, frozen items, fresh food), but I don't think it's so valueable. Could be better to add some mass for freezers, packadge, etc. and make your mission more flexible and able for 2-days flight.
Roscosmos also tried ever faster 3.5-hours rendezvous scheme with Progress MS-07 and Progress MS-08. But there are ever more tight requirements for launch window. As a result, the launch windows were missed in both cases, and the Progresses were launched at 2-day scheme instead.
That factor of the return crew is specifically mentioned in the first social media question they answered after the launch:
Why does it take two days for @Astro_Alex & crew to get to the ISS when it was possible in 6hrs already?
Answer by NASA astronaut Kjell Lindgren:
My understanding is that essentialy because we had the space station, its orbit and phasing, addressed to allow the recent return of the crew, it's just the current position of the space station right now made the launch window such that they had to use this long rendez-vous profile, instead of the shorter profile that we've kind of become used to.