This is the reddit post that makes the most sense to me.
I think that police tampering and clumsy efforts by the real killer caused Steven to be charged. My favorite suspects are Bobby Dassey and Scott Tadych, but you could easily substitute any of the capable men living on the Avery property to fit my theory of the crime.
After entering her car to leave the Avery property, Theresa is stopped by Bobby and Scott as she tries to exit the scrapyard. She is forced at gunpoint to drive to a secluded area. There she is raped and shot in the head. Her body is loaded into the back of the Rav4 and transported to a corner of the scrapyard. The vehicle is hidden here.
Bobby and Scott retrieve a burn barrel and place the body within. They would not have to mutilate the corpse to fit her small frame inside a large barrel. They transport the barrel to the quarry. The body is burned there and the flames remain out of site from passers-by.
The next day, Bobby and/or Scott retrieve the barrel and dump the ashes in the Avery burn pit. At this point they probably are in possession of the Rav4 key by reflexively removing it from the ignition after dumping the Rav4. At this point, neither Bobby nor Scott are actively trying to frame Steven. They are simply covering the crime and disposing of evidence.
After Theresa has been reported missing, Officer Colburn finds the Rav4 on the Avery lot during an illegal search. He uses this opportunity to retrieve Steven Avery's blood from evidence and plant it at the scene. He then suggests to search party leaders that this area is of interest and instructs them not to touch anything if they find the car.
Once the Rav4 has been located by the search party, the area is a crime scene. Officers inform many members of the Avery and Dassey families that Steven is their #1 suspect. Bobby and Scott use this opportunity to further frame Steven by placing the key in his trailer several days into the investigation. They have full knowledge of DNA evidence, since it exonerated Steven once before, so they are careful to clean the key thoroughly.
During the investigation, officers find lots of junk in Steven's trailer, including evidence of his business interaction with Theresa. They also find restraints. Believing Steven to be a deviant, they begin to form a narrative based on rumors of Steven's past and the random items collected in his trailer. This narrative includes restraining and raping Theresa. Note that no physical evidence links Theresa to deviant sexual acts, only the imagination of investigators.
Later in the investigation, human remains are found in the fire pit and the cause of death is determined. Also, Rav4 keys are found in Steven's trailer. At this point, investigators are convinced Steven is guilty, so they attempt to discredit Steven's only alibi witness: Brenden Dassey.
Brenden is a simpleton, but investigators misconstrue his demeanor as consciousness of guilt. They coerce a statement from him that fits the narrative investigators have imagined: A brutal sexual assault followed by an execution. They immediately look for the physical evidence that should be abundant from such a crime.
Investigators find a bullet fragment in the garage of Steven Avery. This fragment lacks Theresa's DNA, but poor handling practices in the forensics lab return a positive result for Theresa's DNA. The technician bends the rules to allow the analysis to stick, believing that the other evidence against Steven is damning enough and the DNA is just another drop in the bucket.
From here, the State has sufficient physical evidence to charge Steven. Constant press conferences from the special prosecutor ensure that the public has a clear narrative to the horrific crime, even if that narrative is only supported by the imagination of investigators and not the physical evidence. The jurors of the trial are familiar with this narrative and attempt to fit the State's evidence to the story they were presented during the news cycle. The State does not present evidence during the trial of sexual assault and imprisonment. None-the-less, the jurors are very aware of the allegations. The defense is unable to adequately refute these rumors because they were not presented at trial.
Steven is found guilty through a combination of inappropriate press releases, popular local animus against the Avery family, and just enough physical evidence to keep the jurors from doubting their verdict.