The first thing you need to know about getting around Scotland is that its geography is a transport planner's worst nightmare. Mountain ranges, high mountain passes, a huge and complex coastline and enormous river gashes show why this used to be a country to sail or walk around.
There are no decent roads. None. Well, perhaps the M74 to England. And this runs out at the border. Much of the rail network was removed in the 1960's creating huge and incomprehensible gaps. Not enough of the country is flat enough to build airports on.
So, having got that sorted out, here's a short guide:
roads - to be avoided around and between the major cities from Mondays to Fridays between 7-10am and 4pm-6pm. The M6/M74 is the only valid road across the border (the A1 and A68 are crash-attracting.) The A9 is the main road north from Edinburgh to Thurso (200 miles) and is generally quite good, but can be dangerous in winter and does cause some dangerous impatience towards Inverness. With every other be very cautious with your driving and don't overtake unless you are certain you can. As we say in Scotland: when yer deid, yer deid a lang time.
trains - generally good but expensive. The best option for most commuting and distance travel between cities. Book in advance and save a lot of money. Book a seat or you might stand. Great service across into England.
buses - are you poor and do you like pain, discomfort and suffering? Yes? Then take the bus. Seriously, the best way to get around the four major cities. Very cheap in most cases but you need exact change. The only way to get to major train-less places like St Andrews, around Edinburgh, the SW and the Borders, but make your journey as short as possible.
ferries - a lovely way (in good weather) to get round the peninsulas and islands of the north and west. There is also a ferry to Europe from Fife. Always book your car in advance.
air - the major airports are Glasgow (international and domestic), Edinburgh (ditto), Glasgow Prestwick International (cheapo flights), Aberdeen and Inverness. There are also airports at Dundee and on many of the islands. Internal flights are very expensive.
walking - the very, very best way to see Scotland. You can walk almost anywhere in the country. BUT - do not go into wilderness areas unless properly prepared as the weather changes very suddenly from the Atlantic.
cycling - avoid the roads. Lots and lots of cycle tracks everywhere.
disabled - most buses, trains and taxis have wheelchair access, But watch that some railway stations can be difficult to access, particularly Edinburgh Waverley, Scotland's busiest.