To make way for other uses of the area
As Yu Zhang notes, any structure built needs to be maintained. The freeway set was composed of timber and plywood, and made to look like concrete, and would need maintenance over time.
This would involve a cost (parts/labour etc.), and it seems likely that if Warner Bros. had felt there was a need for future use of the set, they would have paid for it to remain there.
Following production, and the destruction of the set, it seems that the area has been a potential development location, for retail and housing companies. The Wikipedia article notes several potential projects were in the running even before The Matrix Reloaded was filmed:
Since 2000, the city of Alameda has been planning the redevelopment of the former Naval Air Station, now known as Alameda Point. Complicating the redevelopment are several constraints: land-use constraints consisting of Tidelands Trust; soil and groundwater contamination; wildlife refuge buffer requirements; geotechnical issues; 100-year flood plans; institutional and contractual constraints with Alameda Measure A, the Alameda Naval Air Station Historic District and existing residents and leases.
The latest news (February 20, 2020) suggests that the area will be transformed into a public space:
ALAMEDA (KPIX 5) — This week, the Alameda City Council voted to take a key step in creating a brand new shoreline park that also will include a final resting place for veterans that will be a lot closer to home.
The Council agreed Tuesday to grant a 66-year lease to East Bay Regional Parks to convert the old Alameda Naval Air Station runways into a nature preserve and public space that has views that you can’t buy anywhere.
The old runways aren’t exactly a thing of beauty, but someday soon the 158 acres will be a preserved habitat for seabirds and other wildlife. There will be walking trails and bike paths and a chance for the public to commune with nature, all with an incredible panoramic view of San Francisco just across the bay.
Read the full story here: Alameda Naval Air Station To Be Transformed Into New Shoreline Park