Well at the end of the film, we see Hoyt take the money and he tells Alonzo to 'fuck your appointment with the Russians. You're not going to make it." It ends with Alonzo being gunned down in the street by the Russians and Hoyt pulling in to his driveway of his house and walk inside with the duffel bag full of money.
This seems as though he stole the money so Alonzo would be murdered and he kept the money for himself. However when Hoyt originally went to Alonzo's apartment, he went there to arrest him, when Alonzo asked him where his evidence was he pointed to the money and said 'it's right there.'. So he was going to turn Alonzo in with the bag full of money but Alonzo escaped. He then went to his house most likely to see his wife and child after having such a horrible day with so many near-death experiences.Another theory to tag on there is that during the stand-off in the street when the gang members took Hoyt's side in order for him to leave. Hoyt figured that even with the money as evidence, Alonzo would most likely be acquitted and back to the job, so he would let him die at the hand of the Russians but turn the money in to show that he was corrupt.On a deleted scene included in atleast the R2 dvd, Hoyt says he turned the money in as evidence.In the original script, this is how it endedEXT. JAKE'S HOUSE - NIGHT 86
Jake shoves the nine in his waistband and crosses to the sedan. Lou, Doug and Stan exit the car. They've been
Where's the money, Jake?JAKE
The evidence room at headquarters.
Jake slaps Alonzo's badge on the trunk.STAN
That's not necessary.JAKE
That's not mine.Doug picks up Alonzo's badge, impressed, pockets it. Before Doug can say anything.JAKE
Now leave me the hell alone.With the last of his strength, a battered and mauled Jake
limps away. The three wise men climb in their car. The
plush sedan backs out of Jake's driveway. Jake enters
his house.PULL BACK.
Jake's home becomes indistinguishable in a sea of houses.FADE OUT:THE END