If you look at the record of Republicans voting to fund the FAA since then (22 years is a long time ago), you'll find that they generally haven't been giving the agency the resources they've been asking for, even just to maintain a level of operational effectiveness, nevermind adequately fund a whole new ATC system.
Your link only says, essentially, "congress should have given us more money" and not "evil mustache twirling republicans are the reason for our problems." So, I did look.
The FAA Modernization and Reform Act of 2012 (first I could find post Dubya administration) was, indeed, somewhat contentious (most house democrats voting against the final conference bill, though the senate was less divided). I don't know why the bill was controversial, maybe it was direct funding, but I don't have the data. The FAA Reauthorization Act(s) of 2018 and 2024 were both broadly bipartisan, so I will make the (possibly poor) assumption that 2012 was about other things rather than a specific dollar amount.
From 2009-2024, the democrats have controlled the senate for a total of ten years, the republicans for six. The democrats controlled the house for six years, the republicans for ten. The democrats controlled both houses for four years, the republicans for four years. The democrats controlled the executive for twelve years, the republicans for four (and each with a two year period of full control of government, with the democrats having a ~3 month period of theirs including a filibuster proof senate majority).
So, where is the evidence of your claims that this is a single party problem? Which record should I be looking at?