It is a wish list that the senate has to agree on.

From the link:

"$100 million for underground rail project in Silicon Valley"

Correct.

The bill allots $1.25 billion for federal transit capital investment grants. It does not specify a project in the Silicon Valley. 

Stand for America cites a Fox Business news article that says the language of the bill alludes to $112 million going to phase two of the San Francisco Bay Area Rapid Transit (BART) expansion. The Washington Post also reported that it’s estimated the expansion will receive about $112 million.

The long-planned six-mile extension would include five miles in a subway beneath downtown San Jose, with construction expected to start in 2022 and the line carrying passengers in 2030, accordingto the San Francisco Chronicle. The newspaper says the project’s stimulus funding would be $141 million.