If filing a VFR flight plan will cost $xx in the future, fewer will file them, safety degraded where the rubber meets the road.
If getting clearance for an ILS on a marginal day costs, a percentage that would have will now scud run. Ditto.
If it costs for each trip around the pattern at a controlled airport, well the training mission is going to be cut short.
In the US nowadays over 50% of the future airline pilots come from a GA background. Burdening GA further will have ramifications down the road, beyond the immediate safety issues. Some jobs are inherently a function of the government, not the lowest bidder.