Everyone wants to see the DC Comics based television shows be a part of the overall DC Cinematic Universe, but maybe keeping the movies and tv shows separate is a good thing. Let me explain why.
First off, Marvel's Agents of SHIELD has had a rough start. Season 1 had its issues where it was coming into its own while trying to maintain the story elements from the films. All of this going on while NOT spoiling what happened in films like Captain America: The Winter Soldier, and Thor The Dark World. The second season, SHIELD has come well into its own driving its own stories, and developing material for future Marvel films. It also benefits from being the ONLY Marvel television series that is tied into the overall Marvel Cinematic Universe.
DC is taking a different approach. This approach has not been sitting well with fans. Not only the fans, but also one particular star of one of the CW's top rated shows, Arrow. Stephen Amell has voiced his dislike that DC is not taking Arrow and The Flash, and making them a firm part of the Justice League angle in the films. This would make a LOT of sense, in that DC would not need to focus production money and time into these two characters. However, with Arrow already well established on television with a strong mythos, the Flash is already proving itself as a strong series, as well. Because of this, integrating them into the film universe could prove mildly problematic.
Why problematic? Stephen Amell and Grant Gustin would probably need to take time away from their very busy television production schedules to take part in a very busy production schedule for any Justice League films. Consider that filming for the various movies they would be in would cut directly into their schedule shooting their respective television shows. You would not want to release a film with them in it that the story is reflected in the shows to be released well into the next season, or even a year later.
Also, keep in mind that Marvel's SHIELD has only one major character that may return to the films to bridge them together...possibly...and that is now Director Coulson. None of the actors from the current run of Marvel films have regular spots on SHIELD. Arrow and The Flash do not run in that manner.
Not only that, but any strong villains from the shows would probably end up reserved for the films, thus limiting any potential "events" that could be promoted on the television series'. Characters such as Reverse Flash, or Malcolm Merlyn or Deathstroke are strong villains for both tv series, but would probably end up being reserved for big film antagonists.
DC has decided to approach their properties with a "Multiverse" attitude. This gives creators a LOT of freedom to do a lot with the characters within the confines of their mediums. The drawback? Audience confusion. Seeing that Grant Gustin is already solidifying himself as Barry Allen/The Flash, Ezra Mills will be portraying the very same character in the various films. Personally, since Gustin is already portraying Allen, Mills should be portraying Wally West in the films, as to help deviate and alleviate any confusion of the two character properties.
The positives of allowing the two entities to co-exist in separate 'universes" allows DC to be flexible with their characters. Perhaps allowing DC to push showrunners to "experiment" with particular angles with the characters before pushing them on the movie iterations. Also, keep in mind that an actor may be an excellent actor on television, they don't always work well in movies. Film actors also tend not to do television spots do to either contractual reasons, or personal biases towards television.
All-in-all, creating two universes allows the television producers and the film producers a lot of leeway in the directions they go with the properties, without causing similar issues that SHIELD had during their first season. Also, with a lot of the DC films not coming fully until 2016, it puts a huge restriction on the shows that are already running strong on television. As fans, we also are given a multitude of outlets for our favorite DC characters, allowing us to choose which is our favorite. Would I like to see the television and film versions be in the same universe? Certainly. Realistically, I also see it as near impossible to properly pull off.