Failure is a relative term. The Super Soldier program in the Marvel Cinematic Universe did create notable successes including Captain America. He was everything the military wanted in a soldier; Smart, strong, fast, durable, an asset both tactically and strategically. Unfortunately, they were only able to produce one.
The military will spend money on projects able to produce results that can be replicated. In the case of Captain America and his shield, both were one time events that either lacked resources (vibranium) or particular genius (Erskine) to produce others.
Emil Blonksky's initial transformation appeared successful even though the military used gamma radiation rather than the mysterious Vita Rays used for Captain America. This would later turn the Abomination into a hulking creature unsuitable for most strategic military operations.
The Abomination would have been considered successful overall, he could transform at will, he did follow orders (for a time) and did have the power they desired. But he was ultimately uncontrollable. He was a bomb with legs, killing everything where he landed.
For the military, a weapon that cannot be pointed and completely controlled is of limited strategic value. Tactically a weapon like the Abomination can be dropped somewhere and left to destroy whatever is there but he lacks subtlety, guile and his great size limits his application.
Every attempt to replicate the Super Soldier Serum after Erskine's death has lead to only qualified successes, never without, in some cases, deleterious side effects. Later attempts to create supersoldiers including the Extremis virus, the Deathlock Program and the Centipede Soldiers.
As of 2013, scientists recreated a very similar version of the serum as one of the components of the Centipede Serum, designed to give a person superhuman abilities. This serum was mixed with the Extremis virus, Gamma Radiation and technology from the Chitauri for injection.