You are absolutely daft if you think that's how money works in government. It all goes into a pot and is dolled out according to the budget. When you impose fees like this the fee alone has to be worth it independently.
We should fund training and education in STEM for US citizens but that is a separate discussion from this.
You're wrong both generally and in this case specifically.
Since 1998, H1-B applications include a $500 fee[1] that's used to "...provide training and related activities to workers to assist them in gaining...employment in high-growth industries or economic sectors."[2]
Government programs frequently include provisions for how they will be funded.[3] And revenues generated by government programs are frequently earmarked for specific purposes prior to collection.[4]
That money is not fungible. It is "mandatory" spending.[5]
If you're going to be wrong, you should try not to be rude at the same time.